Re: [gmx-users] energy minimization

[Dallas Warren]

 Gas phase simulations the inter-molecular interactions are smaller, and
intra-molecular interactions dominate. Therefore total energy will be
positive.

If it was filled with a solvent i.e. liquid phase, then inter-molecular
inteactions dominate and the total energy will be negative.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 14 Apr 2020 at 01:59, Afsane Farhadi 
wrote:

> hi friends I generated a box of mixed gas with gmx insert-moleculesI
> ran an energy minimizing.  the potential energy is 4.05e+07 and maximum
> force is 1.25e+03.I used different algorithm likes cg and steep for
> minimization. what do I have to do untill my system potential energy has
> negative value??I need a information about energy minimizing and potential
> energy. I know that positive value of potential energy means the
> intermolecular interaction  is weaker than intramolecular interaction but I
> don't know how I can control this matter. please help
>
> Sent from Yahoo Mail on Android
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Re: [gmx-users] energy minimization in vacuum

[Bratin Kumar Das]

Hi,
 If u minimise the protein in vaccum...the bad contact within the
protein atoms will be removed
After solvation if u do...then both the bad water contact and steric
clashes within the protein will be removed.

On Mon 16 Mar, 2020, 8:37 PM Deepanshi .,  wrote:

> Dear all,
>
> I am trying to simulate an all atom protein in water. I wanted to ask that
> what is the importance of minimizing the protein in a vacuum. It is not
> mentioned in the lysozyme tutorial.
>
> Thanks.
>
> Regards,
> Deepanshi
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Re: [gmx-users] Energy minimization

[Dallas Warren]

This all sounds like
http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc

Remember, the box is just a visualisation of what the system looks like,
and you can move that box anywhere.  What is in the center of the box is
entirely up to you and the post processing you do.  What comes out of the
mdrun engine is arbitrary.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Wed, 26 Feb 2020 at 08:13, Mohamed Abdelaal 
wrote:

> Hello all,
>
> I created a graphene sheet and performed energy minimization, after energy
> minimization I found that parts of the graphene sheet was moved from the
> box bottom to the box topside at the same place (as if it was translated
> upwards). I looked online for the problem and I understood that I should
> restrain the graphene sheet along the z axis. I did that using force =1000.
> and the problem was solved and nothing moved.
>
> After that I tried to insert 25 molecule of (C60) inside a box which
> contains the graphene sheet. I did that and did the energy minimization but
> part of the  graphene sheet moved again from its place although the maximum
> force was less than 1000 which is the force I used to restrain the graphene
> sheet. However I didn't have any error during the energy minimization. Does
> this means that the problem is just in visualization or I might have a
> problem in my energy minimization ?
>
> It is also worth mentioning that the C60 molecules are not spherical as it
> should be. I read about that and I found people mentioning that this shape
> deformation in only a visualization problem and can be solved by using gmx
> trjconv. is it possible that this problem has happened to my whole system
> including the graphene sheet or it shouldn't affect my graphene sheet as
> long as I have restrained it ?
>
> more info:
> I used   periodic_molecules = yes while trying to minimize my whole system.
> (I also tried without it but no impact)
> I wrote:
>
> gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p
> C60_GRM_box.top -o min1.tpr -maxwarn 2
>
> followed by
> gmx mdrun -v -deffnm min1
>
> and I got the below result:
> writing lowest energy coordinates.
>
> Steepest Descents converged to Fmax < 1000 in 3293 steps
> Potential Energy  =  6.3598562e+05
> Maximum force =  9.9486487e+02 on atom 12087
> Norm of force =  6.5454323e+01
>
> Can anybody help me please.
>
> Thanks
>
> Mohamed
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Re: [gmx-users] energy minimization

[Mark Abraham]

Hi,

Typical force fields will have negative energies at minimize
configurations, but my guess is that your initial configuration has some
serious problem. Did you visualise the minimization start and end points?

Mark

On Tue., 27 Aug. 2019, 18:52 Dhrubajyoti Maji,  wrote:

> Dear gromacs users,
>  I am doing energy minimization of a neat urea system. When I set emtol =
> 10 the following result is obtained  :
> Steepest Descents converged to machine precision in 33995 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  =  6.7910172e+04
> Maximum force =  7.8070724e+01 on atom 353
> Norm of force =  3.1714432e+00
> and average energy is
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Potential   72421.6   250014229.1   -16147.4
>  (kJ/mol)
> And when I set emtol=100 the following result is obtained :
> Steepest Descents converged to Fmax < 100 in 12573 steps
> Potential Energy  =  7.1502609e+04
> Maximum force =  8.5925835e+01 on atom 2713
> Norm of force =  5.0333209e+00
> and average energy is
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Potential   77654.4   360022408.3   -22901.6
>  (kJ/mol)
> In both cases the energy is well converged but not less than zero. Does
> only convergence of potential energy (not negative) guarantee the
> completion of EM process ? If so then what emtol value should  I use ?
> Any help will be highly appreciated. Thanks for your time.
> Best regards
> Dhrubajyoti Maji
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Re: [gmx-users] energy minimization

[Dallas Warren]

Look around atom 2016, there is a bad contact between the atoms in that
area, hence the infinite force, very high potential energy, and the
minimisation fails.

On Tue, 25 Sep. 2018, 6:48 pm ikjk, <1761440...@qq.com> wrote:

> hello
>I am doing a md with martini force filed,I create a box, there is a
> double monolayer, then I solvate it, but when I did energy minimization,
>
> gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr  then
>
> NOTE 1 [file minim.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>   your simulation.
>
> Setting the LD random seed to 562058480
> Generated 0 of the 780 non-bonded parameter combinations
> Excluding 1 bonded neighbours molecule type 'DPPC'
> Excluding 1 bonded neighbours molecule type 'W'
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are: 72143  Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 261042.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 168x168x208, spacing 0.118 0.118 0.118
> Estimate for the relative computational
> load of the PME mesh part: 0.91
>
> NOTE 2 [file minim.mdp]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing.
>
>
>
>
>
>
>
>
> gmx mdrun -v -deffnm em
>
>
>
> Steepest Descents:
>Tolerance (Fmax)   =  1.0e+03
>Number of steps=5
> Step=   14, Dmax= 1.2e-06 nm, Epot=  2.36880e+22 Fmax= inf, atom=
> 2016
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
>
> writing lowest energy coordinates.
> it just stopped with 14 steps, here is my mdp file,if you can solve this
> problem, I will appreciate that.
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator  = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol   = 1000.0; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep  = 0.01  ; Minimization step size
> nsteps  = 5 ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and
> long range forces
> cutoff-scheme   = Verlet; Buffered neighbor searching
> ns_type = grid  ; Method to determine neighbor list (simple,
> grid)
> coulombtype = PME   ; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.0   ; Short-range electrostatic cut-off
> rvdw= 1.0   ; Short-range Van der Waals cut-off
> pbc = xyz   ; Periodic Boundary Conditions in all 3
> dimensions
>
>
>
>
>
>
>
>
> jiao
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Re: [gmx-users] energy minimization

[Smith, Micholas D.]

LigParGen generates new atom types for each ligand topology it generates. The 
output files from LigParGen should contain terms for opls800-925 (if necessary) 
in the generated topology file. These need to be included in the force-field 
file you use for use in your simulations. 

A warning should be made about LigParGen: each atom is given a unique atomtype. 
For instance if you have a 25 atom ligand, you will have atomtypes opls 800 
through opls824. Some of these may be repeats. This means that if you want to 
run with a different ligand you have to change these atomtype definitions each 
time.

Hope that helps.


===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Wednesday, July 25, 2018 8:17 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization

On 7/24/18 7:24 AM, farial tavakoli wrote:
> Dear Justin
>
> I used LigParGen server to generate ligand topology but I dont know what 
> changes I have to do in .itp file.
>   when I issued this command:
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor
>
> faced this error:ERROR 1 [file LIG.itp, line 11]:
>Atomtype opls_800 not found
> I checked the aminoacids.rtp file  of  
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not 
> atomtype opls_800 and 801 and ... in this file. while the LIG.itp which 
> generated by LigParGen server has atomtype opls_800 , 801 and ... .
> I have to modify all of these atomtype opls_ in order to correspond to with 
> aminoacid.rtp file?
> I would be thankfull if you help me.
> bestFraial

It looks like your topology introduces new atom types. Check the
LigParGen documentation to see if it requires a different version of the
force field or if the parameters are provided somewhere.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] energy minimization

[Justin Lemkul]

On 7/24/18 7:24 AM, farial tavakoli wrote:

Dear Justin

I used LigParGen server to generate ligand topology but I dont know what 
changes I have to do in .itp file.
  when I issued this command:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor

faced this error:ERROR 1 [file LIG.itp, line 11]:
   Atomtype opls_800 not found
I checked the aminoacids.rtp file  of  
/usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype 
opls_800 and 801 and ... in this file. while the LIG.itp which generated by 
LigParGen server has atomtype opls_800 , 801 and ... .
I have to modify all of these atomtype opls_ in order to correspond to with 
aminoacid.rtp file?
I would be thankfull if you help me.
bestFraial


It looks like your topology introduces new atom types. Check the 
LigParGen documentation to see if it requires a different version of the 
force field or if the parameters are provided somewhere.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] energy minimization

[farial tavakoli]

Dear Justin 

I used LigParGen server to generate ligand topology but I dont know what 
changes I have to do in .itp file. 
 when I issued this command:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor 

faced this error:ERROR 1 [file LIG.itp, line 11]:
  Atomtype opls_800 not found
I checked the aminoacids.rtp file  of  
/usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype 
opls_800 and 801 and ... in this file. while the LIG.itp which generated by 
LigParGen server has atomtype opls_800 , 801 and ... . 
I have to modify all of these atomtype opls_ in order to correspond to with 
aminoacid.rtp file? 
I would be thankfull if you help me.
bestFraial


   On Monday, July 16, 2018, 5:29:17 PM GMT+4:30, Justin Lemkul 
 wrote:  
 
 

On 7/16/18 3:49 AM, farial tavakoli wrote:
>  Dear Justin
>
> Thank you for your reply
> I noticed my problem ( the reason was topolgen.pl name in my directory, it is 
> named topologen_1.1.pl in the working directory)
> I generated my ligand topology but got this :
> No output type specified. Using default type of .top
> Unknown atom type: N 13 with 2 bonds - cannot assign atom type.
> Using default H type for atom 16.
> Using default H type for atom 26.
> Using default H type for atom 31.
> Using default H type for atom 38.
> Using default H type for atom 39.
> Using default H type for atom 40.
> Using default H type for atom 41.
> Unknown atom type: N 42 with 2 bonds - cannot assign atom type.
> Using default H type for atom 47.
> Using default H type for atom 48.
> Using default H type for atom 49.
> Using default H type for atom 50.
> Using default H type for atom 51.
> Using default H type for atom 52.
>
> 
> WARNING: Net charge on the molecule is -2.781
> You will need to make corrections to the output topology
> 
>
> TopolGen, version 1.1_dev (10/14/2009) complete.
>
> Output topology has been written. An attempt has been made to assign charges 
> and atom types based
> on existing functional groups, but they may not be correct.  No charge 
> calculations or other
> parameterization calculations have been done.  Guesses have been made for 
> charge groups.  Please
> inspect and correct the topology before using it in any simulations.  The 
> author of the script does
> NOT guarantee accuracy or usability of any of the content; TopolGen was 
> written as a convenience
> for outputting a skeleton topology, and nothing more.

Heed the above warning. TopolGen assigns parameters based on similarity 
to known functional groups. If your molecule has something unusual, it 
makes no attempt to try to assign reasonable parameters. You'll need to 
actually parametrize the molecule. Make use of available web servers 
like LikeParGen or others.

-Justin

>
> the N13 atom connected to C with double bond. it sounds topolgen can not 
> identify N atom in 2 bonds with C .
> would you please help me to figure out this problem
> thans in advanceFarial
>
>      On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul 
> wrote:
>  
>  
>
> On 7/15/18 1:38 AM, farial tavakoli wrote:
>>    Dear Justin
>>
>> But I copied & pasted topolgen and perl5 folders in the working directory. 
>> and faced the mentioned error.
>>
>> Can't open perl script "topolgen.pl": No such file or directory
>> I dont know how I should figure out this problem.
> The problem is still the same: there's nothing called "topolgen.pl" in
> the working directory. List your files, you'll see it's called something
> else.
>
>> Which one of all-atom force fields will you choose to run a simulation on a 
>> complex with small molecule, if you want to calculate binding energy using 
>> G_MMPBSA ?I really need your guidance .
> Presumably any of them, but I don't do such calculations.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] energy minimization

[Justin Lemkul]

On 7/16/18 3:49 AM, farial tavakoli wrote:

  Dear Justin

Thank you for your reply
I noticed my problem ( the reason was topolgen.pl name in my directory, it is 
named topologen_1.1.pl in the working directory)
I generated my ligand topology but got this :
No output type specified. Using default type of .top
Unknown atom type: N 13 with 2 bonds - cannot assign atom type.
Using default H type for atom 16.
Using default H type for atom 26.
Using default H type for atom 31.
Using default H type for atom 38.
Using default H type for atom 39.
Using default H type for atom 40.
Using default H type for atom 41.
Unknown atom type: N 42 with 2 bonds - cannot assign atom type.
Using default H type for atom 47.
Using default H type for atom 48.
Using default H type for atom 49.
Using default H type for atom 50.
Using default H type for atom 51.
Using default H type for atom 52.


WARNING: Net charge on the molecule is -2.781
You will need to make corrections to the output topology


TopolGen, version 1.1_dev (10/14/2009) complete.

Output topology has been written. An attempt has been made to assign charges 
and atom types based
on existing functional groups, but they may not be correct.  No charge 
calculations or other
parameterization calculations have been done.  Guesses have been made for 
charge groups.  Please
inspect and correct the topology before using it in any simulations.  The 
author of the script does
NOT guarantee accuracy or usability of any of the content; TopolGen was written 
as a convenience
for outputting a skeleton topology, and nothing more.


Heed the above warning. TopolGen assigns parameters based on similarity 
to known functional groups. If your molecule has something unusual, it 
makes no attempt to try to assign reasonable parameters. You'll need to 
actually parametrize the molecule. Make use of available web servers 
like LikeParGen or others.


-Justin



the N13 atom connected to C with double bond. it sounds topolgen can not 
identify N atom in 2 bonds with C .
would you please help me to figure out this problem
thans in advanceFarial

 On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul 
 wrote:
  
  


On 7/15/18 1:38 AM, farial tavakoli wrote:

   Dear Justin

But I copied & pasted topolgen and perl5 folders in the working directory. and 
faced the mentioned error.

Can't open perl script "topolgen.pl": No such file or directory
I dont know how I should figure out this problem.

The problem is still the same: there's nothing called "topolgen.pl" in
the working directory. List your files, you'll see it's called something
else.


Which one of all-atom force fields will you choose to run a simulation on a 
complex with small molecule, if you want to calculate binding energy using 
G_MMPBSA ?I really need your guidance .

Presumably any of them, but I don't do such calculations.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] energy minimization

[farial tavakoli]

 Dear Justin 

Thank you for your reply
I noticed my problem ( the reason was topolgen.pl name in my directory, it is 
named topologen_1.1.pl in the working directory) 
I generated my ligand topology but got this :
No output type specified. Using default type of .top
Unknown atom type: N 13 with 2 bonds - cannot assign atom type.
Using default H type for atom 16.
Using default H type for atom 26.
Using default H type for atom 31.
Using default H type for atom 38.
Using default H type for atom 39.
Using default H type for atom 40.
Using default H type for atom 41.
Unknown atom type: N 42 with 2 bonds - cannot assign atom type.
Using default H type for atom 47.
Using default H type for atom 48.
Using default H type for atom 49.
Using default H type for atom 50.
Using default H type for atom 51.
Using default H type for atom 52.


WARNING: Net charge on the molecule is -2.781
You will need to make corrections to the output topology


TopolGen, version 1.1_dev (10/14/2009) complete.

Output topology has been written. An attempt has been made to assign charges 
and atom types based
on existing functional groups, but they may not be correct.  No charge 
calculations or other 
parameterization calculations have been done.  Guesses have been made for 
charge groups.  Please
inspect and correct the topology before using it in any simulations.  The 
author of the script does 
NOT guarantee accuracy or usability of any of the content; TopolGen was written 
as a convenience 
for outputting a skeleton topology, and nothing more.


the N13 atom connected to C with double bond. it sounds topolgen can not 
identify N atom in 2 bonds with C . 
would you please help me to figure out this problem
thans in advanceFarial

On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul 
 wrote:  
 
 

On 7/15/18 1:38 AM, farial tavakoli wrote:
>  Dear Justin
>
> But I copied & pasted topolgen and perl5 folders in the working directory. 
> and faced the mentioned error.
>
> Can't open perl script "topolgen.pl": No such file or directory
> I dont know how I should figure out this problem.

The problem is still the same: there's nothing called "topolgen.pl" in 
the working directory. List your files, you'll see it's called something 
else.

> Which one of all-atom force fields will you choose to run a simulation on a 
> complex with small molecule, if you want to calculate binding energy using 
> G_MMPBSA ?I really need your guidance .

Presumably any of them, but I don't do such calculations.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] energy minimization

[Justin Lemkul]

On 7/15/18 1:38 AM, farial tavakoli wrote:

  Dear Justin

But I copied & pasted topolgen and perl5 folders in the working directory. and 
faced the mentioned error.

Can't open perl script "topolgen.pl": No such file or directory
I dont know how I should figure out this problem.


The problem is still the same: there's nothing called "topolgen.pl" in 
the working directory. List your files, you'll see it's called something 
else.



Which one of all-atom force fields will you choose to run a simulation on a 
complex with small molecule, if you want to calculate binding energy using 
G_MMPBSA ?I really need your guidance .


Presumably any of them, but I don't do such calculations.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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* Please search the archive at 
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Re: [gmx-users] energy minimization

[farial tavakoli]

 Dear Justin 

But I copied & pasted topolgen and perl5 folders in the working directory. and 
faced the mentioned error. 

Can't open perl script "topolgen.pl": No such file or directory
I dont know how I should figure out this problem. 
Which one of all-atom force fields will you choose to run a simulation on a 
complex with small molecule, if you want to calculate binding energy using 
G_MMPBSA ?I really need your guidance .
best 
Farial
On Saturday, July 14, 2018, 6:35:27 PM GMT+4:30, Justin Lemkul 
 wrote:  
 
 

On 7/14/18 5:03 AM, farial tavakoli wrote:
>  
> Dear justin
>
> I am trying to run a simulation on my complex which has small molecule as a 
> ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then 
> installed perl script on linux. then typed "perl -v" to check if it is 
> installed. the perl 5.20.1 was installed.
> but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type 
> itp/top] " command to generate ligand topology , faced with this error:
> Can't open perl script "topolgen.pl": No such file or directory
> Infact I am new user in generation topology for small molecules using OPLSAA 
> ff. Would you please  help me to figure out this problem?

"No such file or directory" means the file isn't in the working 
directory. This is a generic error message from your shell and nothing 
specific about the script itself.

-Justin
>
> Farial
> best
>      On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul 
> wrote:
>  
>  
>
> On 2/20/18 12:52 PM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>>!important; }  Dear Justin
>> Thank you for the reply
>> You meant , to tweak the emtol doesn't have noticable affects on the 
>> conformational enssemble generated by MD?
>>    
> Precisely what I said, yes.
>
> -Justin
>
>> Sent from Yahoo Mail for iPhone
>>
>>
>> On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul  
>> wrote:
>>
>>
>>
>> On 2/20/18 4:52 AM, farial tavakoli wrote:
>>> Dear GMX users
>>> I used CHARMM36 all atom force field to generate .top and .gro files for my 
>>> complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
>>> residues, then ran a md simulation on it and then used g_mmpbsa to 
>>> calculate the binding free energy by pdies ( 2 and 4) but got + 426 and 
>>> +527 kjol/mol, respectively. While, I calculated binding energy before for 
>>> many other complexes without any phosphate groups using OPLS all atom force 
>>> field and pdie = 2 and obtained minus energy. But this time , I dont know 
>>> why I got positive binding energy? Is it because of charmm36 all atom force 
>>> field , the phosphate groups or it is needed to be energy minimized under 
>>> more restriction situations?
>>> I am checking different factors to understand its reason, so I wanted to 
>>> know , would it be ok if I energy minimize the complex with more 
>>> restriction situations ? for example by specifying emtol under 1000 
>>> kj/mol/nm , like 800 ? I think the positive binding energy might be because 
>>> of the complex didnt minimized well. however I checked the em.log file and 
>>> saw it was minimized well:
>>>
>>> Steepest Descents converged to Fmax < 1000 in 241 steps
>>> Potential Energy  = -6.5047744e+05
>>> Maximum force =  9.8285083e+02 on atom 3335
>>> Norm of force =  3.6905827e+01
>>> Is there anyone can advice me in energy minimization with emtol 800?
>> The purpose of energy minimization is to establish a reasonable starting
>> point for your simulation. Tweaks to emtol will have little to no
>> noticeable bearing on the conformational ensemble generated by MD.
>>
>> -Justin
>>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] energy minimization

[Justin Lemkul]

On 7/14/18 5:03 AM, farial tavakoli wrote:
  
Dear justin


I am trying to run a simulation on my complex which has small molecule as a ligand , 
using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then installed perl script on 
linux. then typed "perl -v" to check if it is installed. the perl 5.20.1 was 
installed.
but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type itp/top] 
" command to generate ligand topology , faced with this error:
Can't open perl script "topolgen.pl": No such file or directory
Infact I am new user in generation topology for small molecules using OPLSAA 
ff. Would you please  help me to figure out this problem?


"No such file or directory" means the file isn't in the working 
directory. This is a generic error message from your shell and nothing 
specific about the script itself.


-Justin


Farial
best
 On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul 
 wrote:
  
  


On 2/20/18 12:52 PM, farial tavakoli wrote:

   blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear Justin
Thank you for the reply
You meant , to tweak the emtol doesn't have noticable affects on the 
conformational enssemble generated by MD?
   

Precisely what I said, yes.

-Justin


Sent from Yahoo Mail for iPhone


On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul  wrote:



On 2/20/18 4:52 AM, farial tavakoli wrote:

Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my 
complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
respectively. While, I calculated binding energy before for many other 
complexes without any phosphate groups using OPLS all atom force field and pdie 
= 2 and obtained minus energy. But this time , I dont know why I got positive 
binding energy? Is it because of charmm36 all atom force field , the phosphate 
groups or it is needed to be energy minimized under more restriction situations?
I am checking different factors to understand its reason, so I wanted to know , 
would it be ok if I energy minimize the complex with more restriction 
situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? 
I think the positive binding energy might be because of the complex didnt 
minimized well. however I checked the em.log file and saw it was minimized well:

Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy  = -6.5047744e+05
Maximum force =  9.8285083e+02 on atom 3335
Norm of force =  3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800?

The purpose of energy minimization is to establish a reasonable starting
point for your simulation. Tweaks to emtol will have little to no
noticeable bearing on the conformational ensemble generated by MD.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Energy minimization of solvated MOFs.

[Dallas Warren]

Have you visualised the system to see what it is about that water that
is generating such a high force?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Wed, 11 Jul 2018 at 00:57, Nagasree Garapati
 wrote:
>
>
> Hi
>
>
> I am trying to run some simulations on Metal-Organic frameworks like ZIF-8. I 
> have obtained both structure file (from CCDC) and forcefield data from 
> literature and I was able to successfully run energy minimization, and 
> equilibirum MD (NVT and NPT) simulations on the crystal structure of MOF. But 
> when I tried to perform energy minimization for a system of MOF in water (by 
> putting MOF in a box and solvating using gmx solvate), I am getting following 
> message and forces are very high on water molecules. I am not how to overcome 
> this problem, any thoughts are appreciated.
>
>
> "Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 5 (which may not be possible for your system). It
> stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 95 steps,
> but did not reach the requested Fmax < 5.
> Potential Energy  = -3.38556029741624e+13
> Maximum force =  2.45386477264935e+25 on atom 306
> Norm of force =  1.49337454338593e+24"
>
>
>
> Thank You
>
>
>
> With Regards
> Nagasree Garapati
> Research Assistant Professor
> Dept of Chemical and Biomedical Engineering
> West Virginia University
> PO Box 6102
> Morgantown, WV 26506-6102
> 304 293-5028(O)
> 304 276-3674(M)
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
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>
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>
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Re: [gmx-users] energy minimization

[farial tavakoli]

Dear Justin
In according to obtaining positive binding free energy using g_mmpbsa for my 
complex which has 2 phosphotyrosine residues and is simulated by charmm36 force 
field , I sent an email to g_mmpbsa mailing list and informed them to help me 
for solving my problem, but they replied me : " we have not tested the g_mmpbsa 
with charmm36 so we can't say about the validity. Other members of g_mmpbsa 
tool, also previously reported about the positive binding energy when using 
charmm36 force field." I sent another email to them :would you please advice me 
how could I calculate the  free binding energy of my complex (receptor and 
ligand that has 2 phosphotyrosine residues ) which has been simulated by 
charmm36 all atom force field? but I have not any response yet.
 so I decided to use a modified amber99s force field to use in gromacs to 
simulate my complex. and then use g_mmpbsa to calculate the binding energy. I 
searched the net and found this one to modify the amber99s ff : 
http://www.pharmacy.manchester.ac.uk/bryce/amberbut it is not for gromacs. 
Would you please advice me how can I get a modified amber force field to 
simulate my complex using gromacs?or help me how  can I calcualte the binding 
energy of my complex which is simulated by charmm36 in gromacs?
with best regardsFarial
 

On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul 
 wrote:  
 
 

On 2/20/18 12:52 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear Justin
> Thank you for the reply
> You meant , to tweak the emtol doesn't have noticable affects on the 
> conformational enssemble generated by MD?
>  

Precisely what I said, yes.

-Justin

>
> Sent from Yahoo Mail for iPhone
>
>
> On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul  wrote:
>
>
>
> On 2/20/18 4:52 AM, farial tavakoli wrote:
>> Dear GMX users
>> I used CHARMM36 all atom force field to generate .top and .gro files for my 
>> complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
>> residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
>> the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
>> respectively. While, I calculated binding energy before for many other 
>> complexes without any phosphate groups using OPLS all atom force field and 
>> pdie = 2 and obtained minus energy. But this time , I dont know why I got 
>> positive binding energy? Is it because of charmm36 all atom force field , 
>> the phosphate groups or it is needed to be energy minimized under more 
>> restriction situations?
>> I am checking different factors to understand its reason, so I wanted to 
>> know , would it be ok if I energy minimize the complex with more restriction 
>> situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 
>> ? I think the positive binding energy might be because of the complex didnt 
>> minimized well. however I checked the em.log file and saw it was minimized 
>> well:
>>
>> Steepest Descents converged to Fmax < 1000 in 241 steps
>> Potential Energy  = -6.5047744e+05
>> Maximum force =  9.8285083e+02 on atom 3335
>> Norm of force =  3.6905827e+01
>> Is there anyone can advice me in energy minimization with emtol 800?
> The purpose of energy minimization is to establish a reasonable starting
> point for your simulation. Tweaks to emtol will have little to no
> noticeable bearing on the conformational ensemble generated by MD.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] energy minimization

[Justin Lemkul]

On 2/20/18 12:52 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear Justin
Thank you for the reply
You meant , to tweak the emtol doesn't have noticable affects on the 
conformational enssemble generated by MD?
  


Precisely what I said, yes.

-Justin



Sent from Yahoo Mail for iPhone


On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul  wrote:



On 2/20/18 4:52 AM, farial tavakoli wrote:

Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my 
complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
respectively. While, I calculated binding energy before for many other 
complexes without any phosphate groups using OPLS all atom force field and pdie 
= 2 and obtained minus energy. But this time , I dont know why I got positive 
binding energy? Is it because of charmm36 all atom force field , the phosphate 
groups or it is needed to be energy minimized under more restriction situations?
I am checking different factors to understand its reason, so I wanted to know , 
would it be ok if I energy minimize the complex with more restriction 
situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? 
I think the positive binding energy might be because of the complex didnt 
minimized well. however I checked the em.log file and saw it was minimized well:

Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy  = -6.5047744e+05
Maximum force =  9.8285083e+02 on atom 3335
Norm of force =  3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800?

The purpose of energy minimization is to establish a reasonable starting
point for your simulation. Tweaks to emtol will have little to no
noticeable bearing on the conformational ensemble generated by MD.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] energy minimization

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear Justin
Thank you for the reply
You meant , to tweak the emtol doesn't have noticable affects on the 
conformational enssemble generated by MD? 
 

Sent from Yahoo Mail for iPhone


On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul  wrote:



On 2/20/18 4:52 AM, farial tavakoli wrote:
> Dear GMX users
> I used CHARMM36 all atom force field to generate .top and .gro files for my 
> complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
> residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
> the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
> respectively. While, I calculated binding energy before for many other 
> complexes without any phosphate groups using OPLS all atom force field and 
> pdie = 2 and obtained minus energy. But this time , I dont know why I got 
> positive binding energy? Is it because of charmm36 all atom force field , the 
> phosphate groups or it is needed to be energy minimized under more 
> restriction situations?
> I am checking different factors to understand its reason, so I wanted to know 
> , would it be ok if I energy minimize the complex with more restriction 
> situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 
> ? I think the positive binding energy might be because of the complex didnt 
> minimized well. however I checked the em.log file and saw it was minimized 
> well:
>
> Steepest Descents converged to Fmax < 1000 in 241 steps
> Potential Energy  = -6.5047744e+05
> Maximum force =  9.8285083e+02 on atom 3335
> Norm of force =  3.6905827e+01
> Is there anyone can advice me in energy minimization with emtol 800?

The purpose of energy minimization is to establish a reasonable starting 
point for your simulation. Tweaks to emtol will have little to no 
noticeable bearing on the conformational ensemble generated by MD.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] energy minimization

[Justin Lemkul]

On 2/20/18 4:52 AM, farial tavakoli wrote:

Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my 
complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
respectively. While, I calculated binding energy before for many other 
complexes without any phosphate groups using OPLS all atom force field and pdie 
= 2 and obtained minus energy. But this time , I dont know why I got positive 
binding energy? Is it because of charmm36 all atom force field , the phosphate 
groups or it is needed to be energy minimized under more restriction situations?
I am checking different factors to understand its reason, so I wanted to know , 
would it be ok if I energy minimize the complex with more restriction 
situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? 
I think the positive binding energy might be because of the complex didnt 
minimized well. however I checked the em.log file and saw it was minimized well:

Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy  = -6.5047744e+05
Maximum force =  9.8285083e+02 on atom 3335
Norm of force =  3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800?


The purpose of energy minimization is to establish a reasonable starting 
point for your simulation. Tweaks to emtol will have little to no 
noticeable bearing on the conformational ensemble generated by MD.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] energy minimization

[rose rahmani]

On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul  wrote:

>
>
> On 1/6/18 10:10 AM, rose rahmani wrote:
>
>> Hi,
>>
>> I want to calculate the number of density profile of water.the initial
>> .gro
>> file which i have,has amino acid in itself, which should not be present in
>> this analyze. So, i had to remove amino acid, and then, when i wanted to
>> do
>> energy minimization again, it's crushed and gave me step files.
>> maybe it's because of modifying the initial gro file but i didn't have any
>> choice i think so! because i have another structures in initial.gro file
>> which i don't want to modify their coordinates.and all structure are in
>> the
>> center of box and the rest of the box should be empty.
>> would you please help me? what is the alternative?
>>
>
> Why do you have to remove the amino acid to do this analysis?

I should study different amino acids one by one in my system.In literature
there is just  one NUMBER density profile scheme reported for all
different( in amino acids) tests. This means that this profile should  not
depend on amino acids and should be token before amino acid is in. it's
rational because as you said amino acid can change the distribution of
water also its number density so different amino acids cause different
changes, am i wrong?
However in literature a few distance above surface is considered (1nm) and
my amino acids are in about 1.7 far from surface ( because i want to do
pulling in next step)but i think it's better to remove it( as i have not
access to file before amino acid is in so i thought maybe it's better to
remove it and do EM and equilibration again). What do you think,sir?
BTW, how can i specify the gmx density to just calculate the specific
distance above surface not whole box (Z dimension) ?

Thank you

>

You're creating a rather large void, which will make nearby waters
> unstable. In the analysis, you're going to have a volume occupied by the
> amino acid that yields zero water density. That's going to happen
> irrespective of whether or not you remove the amino acid, so save yourself
> some trouble and don't mess with the coordinates.
>
> -Justin
>
>
> with regards
>>
>>
>>
>>
>> this is em.job
>>
>> Steepest Descents:
>> Tolerance (Fmax)   =  1.0e+01
>> Number of steps= 5000
>> Step=0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom=
>> 815
>> Step=1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom=
>> 4307
>> Step=2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom=
>> 4307
>> Step=3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom=
>> 4302
>> Step=4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom=
>> 4303
>> Step=5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom=
>> 4303
>> Step=6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom=
>> 4303
>> Step=7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom=
>> 4303
>> Step=8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom=
>> 4303
>> Step=9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom=
>> 4303
>> Step=   10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom=
>> 4302
>> Step=   11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom=
>> 4302
>> Step=   12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom=
>> 4301
>> Step=   13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom=
>> 4303
>>
>> step 14: Water molecule starting at atom 2018 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>>
>> step 14: Water molecule starting at atom 1265 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>> Wrote pdb files with previous and current coordinates
>> Wrote pdb files with previous and current coordinates
>> Step=   14, Dmax= 1.1e-01 nm, Epot=  2.77257e+05 Fmax= 2.29207e+09, atom=
>> 2018^M
>> step 15: Water molecule starting at atom 1331 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>> Wrote pdb files with previous and current coordinates
>> Step=   15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom=
>> 1331^MStep=   16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02,
>> atom= 4301
>> Step=   17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom=
>> 4303
>> Step=   18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom=
>> 4301
>> Step=   19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom=
>> 4301
>> Step=   20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom=
>> 4301
>> Step=   21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom=
>> 4301
>>
>> 140,1
>> .
>> .
>> .
>> .
>>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of 

Re: [gmx-users] energy minimization

[Justin Lemkul]

On 1/6/18 10:10 AM, rose rahmani wrote:

Hi,

I want to calculate the number of density profile of water.the initial .gro
file which i have,has amino acid in itself, which should not be present in
this analyze. So, i had to remove amino acid, and then, when i wanted to do
energy minimization again, it's crushed and gave me step files.
maybe it's because of modifying the initial gro file but i didn't have any
choice i think so! because i have another structures in initial.gro file
which i don't want to modify their coordinates.and all structure are in the
center of box and the rest of the box should be empty.
would you please help me? what is the alternative?


Why do you have to remove the amino acid to do this analysis? You're 
creating a rather large void, which will make nearby waters unstable. In 
the analysis, you're going to have a volume occupied by the amino acid 
that yields zero water density. That's going to happen irrespective of 
whether or not you remove the amino acid, so save yourself some trouble 
and don't mess with the coordinates.


-Justin


with regards




this is em.job

Steepest Descents:
Tolerance (Fmax)   =  1.0e+01
Number of steps= 5000
Step=0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom=
815
Step=1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom=
4307
Step=2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom=
4307
Step=3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom=
4302
Step=4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom=
4303
Step=5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom=
4303
Step=6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom=
4303
Step=7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom=
4303
Step=8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom=
4303
Step=9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom=
4303
Step=   10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom=
4302
Step=   11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom=
4302
Step=   12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom=
4301
Step=   13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom=
4303

step 14: Water molecule starting at atom 2018 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 14: Water molecule starting at atom 1265 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=   14, Dmax= 1.1e-01 nm, Epot=  2.77257e+05 Fmax= 2.29207e+09, atom=
2018^M
step 15: Water molecule starting at atom 1331 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom=
1331^MStep=   16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02,
atom= 4301
Step=   17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom=
4303
Step=   18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom=
4301
Step=   19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom=
4301
Step=   20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom=
4301
Step=   21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom=
4301

140,1
.
.
.
.


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Energy Minimization Error

[Amali Guruge]

Dear Gromacs users,

When I tried to run the equilibration run, it gave several LINCS WARNINGS.
However, that equilibration run is completed by the Gromacs. Do I have to
concern about these warnings or can I ignore those?

Thank you.

Sincerely,
A. Guruge

On Fri, Oct 20, 2017 at 11:22 AM, Justin Lemkul  wrote:

>
>
> On 10/19/17 8:21 PM, Amali Guruge wrote:
>
>> Dear Gromacs users,
>>
>> Thank you very much for the reply. My concern is "step 11: One or more
>> water molecules can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate". What
>> should I do to avoid it?
>>
>
> That happens often during minimization, especially the early steps. If it
> doesn't come back up again, it's fine. It should never happen during MD.
>
> -Justin
>
>
> Thank you.
>>
>> On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul  wrote:
>>
>>
>>> On 10/19/17 8:10 PM, Amali Guruge wrote:
>>>
>>> Dear Gromacs Users,

 I tried to energy minimize my system using the steep integrator.
 However,
 it gave the following message.

 Steepest Descents:
  Tolerance (Fmax)   =  5.0e+02
  Number of steps= 2000
 Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06,
 atom=
 14611
 Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05,
 atom=
 18527
 Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05,
 atom=
 1005
 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04,
 atom=
 6994
 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04,
 atom=
 58902
 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04,
 atom=
 515
 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04,
 atom=
 188631
 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04,
 atom=
 188631
 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04,
 atom=
 188631
 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04,
 atom=
 188631
 Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04,
 atom=
 188631

 step 11: One or more water molecules can not be settled.
 Check for bad contacts and/or reduce the timestep if appropriate.

 After 2000 steps it says,

 Steepest Descents did not converge to Fmax < 500 in 2001 steps.
 Potential Energy  = -4.6310655e+06
 Maximum force =  6.7453154e+03 on atom 18769
 Norm of force =  3.3632809e+01

 Simulation ended prematurely, no performance report will be written.


 my em.mdp file contains following parameters.

 integrator=  steep; simulation algorithm
 dt=  0.002; time step (ps)
 nsteps=  2000; # steps
 comm_mode=  linear; c.o.m. motion reset
 ;
 ;Energy Minimization
 emtol=  500; converged F lt value (kJ mol-1
 nm-1)
 emstep=  0.01 ; initial step size (nm)
 ;
 ;Output Control
 nstxout=  5 ; write coordinates to .trr
 nstvout=  5; write velocities to .trr
 nstlog=  5; write energies to .log
 nstenergy=  1; write energies to .edr
 ;
 ;Neightbour Searching
 cutoff-scheme   =  Verlet; scheme used for
 generating pair list
 nstlist =  10   ; update neighbour list
 ns_type=  grid; neighbour list method
 pbc=  xyz; periodic boundary conditions
 rlist=  0.9 ; cut-off for short-range neighbour
 (nm)
 ;
 ;Electrostatics and VdW
 coulombtype=  PME; type of coulomb interaction
 rcoulomb=  0.9; cut-off distance for coulomb
 epsilon_r=  1; dielectric constant
 rvdw=  0.9; cut-off for vdw
 fourierspacing=  0.12; maximum grid spacing for FFT
 pme_order=  4; interpolation order for PME
 ewald_rtol=  1e-5; relative strength of
 Ewald-shifted
 DispCorr=  EnerPres ; long range dispersion
 corrections
 ;
 ;Temperature Coupling
 Tcoupl=  no; type of temperature coupling
 ;
 ;Pressure Coupling
 Pcoupl=  no ; type of pressure coupling
 ;
 ;Velocity Generation
 gen_vel=  no ; generate initial velocities
 ;
 ;Bonds
 constraints=  none; bond constraint type

 I used gmx solvate to add water 

Re: [gmx-users] Energy Minimization Error

[Justin Lemkul]

On 10/19/17 8:21 PM, Amali Guruge wrote:

Dear Gromacs users,

Thank you very much for the reply. My concern is "step 11: One or more
water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate". What
should I do to avoid it?


That happens often during minimization, especially the early steps. If 
it doesn't come back up again, it's fine. It should never happen during MD.


-Justin


Thank you.

On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul  wrote:



On 10/19/17 8:10 PM, Amali Guruge wrote:


Dear Gromacs Users,

I tried to energy minimize my system using the steep integrator. However,
it gave the following message.

Steepest Descents:
 Tolerance (Fmax)   =  5.0e+02
 Number of steps= 2000
Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06, atom=
14611
Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05, atom=
18527
Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05, atom=
1005
Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
6994
Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
58902
Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
515
Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
188631
Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
188631
Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
188631
Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
188631
Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
188631

step 11: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

After 2000 steps it says,

Steepest Descents did not converge to Fmax < 500 in 2001 steps.
Potential Energy  = -4.6310655e+06
Maximum force =  6.7453154e+03 on atom 18769
Norm of force =  3.3632809e+01

Simulation ended prematurely, no performance report will be written.


my em.mdp file contains following parameters.

integrator=  steep; simulation algorithm
dt=  0.002; time step (ps)
nsteps=  2000; # steps
comm_mode=  linear; c.o.m. motion reset
;
;Energy Minimization
emtol=  500; converged F lt value (kJ mol-1 nm-1)
emstep=  0.01 ; initial step size (nm)
;
;Output Control
nstxout=  5 ; write coordinates to .trr
nstvout=  5; write velocities to .trr
nstlog=  5; write energies to .log
nstenergy=  1; write energies to .edr
;
;Neightbour Searching
cutoff-scheme   =  Verlet; scheme used for
generating pair list
nstlist =  10   ; update neighbour list
ns_type=  grid; neighbour list method
pbc=  xyz; periodic boundary conditions
rlist=  0.9 ; cut-off for short-range neighbour
(nm)
;
;Electrostatics and VdW
coulombtype=  PME; type of coulomb interaction
rcoulomb=  0.9; cut-off distance for coulomb
epsilon_r=  1; dielectric constant
rvdw=  0.9; cut-off for vdw
fourierspacing=  0.12; maximum grid spacing for FFT
pme_order=  4; interpolation order for PME
ewald_rtol=  1e-5; relative strength of Ewald-shifted
DispCorr=  EnerPres ; long range dispersion
corrections
;
;Temperature Coupling
Tcoupl=  no; type of temperature coupling
;
;Pressure Coupling
Pcoupl=  no ; type of pressure coupling
;
;Velocity Generation
gen_vel=  no ; generate initial velocities
;
;Bonds
constraints=  none; bond constraint type

I used gmx solvate to add water molecules to the system.

How could I get rid of bad contacts of water molecules? Appreciate if
anyone help me to solve the problem.


mdrun stopped after 2000 steps because you told it to. You need to
minimize further, so increase nsteps (or set it to -1 to let mdrun go as
long as it needs to without having to guess a number).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] Energy Minimization Error

[Amali Guruge]

Dear Gromacs users,

Thank you very much for the reply. My concern is "step 11: One or more
water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate". What
should I do to avoid it?

Thank you.

On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul  wrote:

>
>
> On 10/19/17 8:10 PM, Amali Guruge wrote:
>
>> Dear Gromacs Users,
>>
>> I tried to energy minimize my system using the steep integrator. However,
>> it gave the following message.
>>
>> Steepest Descents:
>> Tolerance (Fmax)   =  5.0e+02
>> Number of steps= 2000
>> Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06, atom=
>> 14611
>> Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05, atom=
>> 18527
>> Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05, atom=
>> 1005
>> Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
>> 6994
>> Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
>> 58902
>> Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
>> 515
>> Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
>> 188631
>> Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
>> 188631
>> Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
>> 188631
>> Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
>> 188631
>> Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
>> 188631
>>
>> step 11: One or more water molecules can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>>
>> After 2000 steps it says,
>>
>> Steepest Descents did not converge to Fmax < 500 in 2001 steps.
>> Potential Energy  = -4.6310655e+06
>> Maximum force =  6.7453154e+03 on atom 18769
>> Norm of force =  3.3632809e+01
>>
>> Simulation ended prematurely, no performance report will be written.
>>
>>
>> my em.mdp file contains following parameters.
>>
>> integrator=  steep; simulation algorithm
>> dt=  0.002; time step (ps)
>> nsteps=  2000; # steps
>> comm_mode=  linear; c.o.m. motion reset
>> ;
>> ;Energy Minimization
>> emtol=  500; converged F lt value (kJ mol-1 nm-1)
>> emstep=  0.01 ; initial step size (nm)
>> ;
>> ;Output Control
>> nstxout=  5 ; write coordinates to .trr
>> nstvout=  5; write velocities to .trr
>> nstlog=  5; write energies to .log
>> nstenergy=  1; write energies to .edr
>> ;
>> ;Neightbour Searching
>> cutoff-scheme   =  Verlet; scheme used for
>> generating pair list
>> nstlist =  10   ; update neighbour list
>> ns_type=  grid; neighbour list method
>> pbc=  xyz; periodic boundary conditions
>> rlist=  0.9 ; cut-off for short-range neighbour
>> (nm)
>> ;
>> ;Electrostatics and VdW
>> coulombtype=  PME; type of coulomb interaction
>> rcoulomb=  0.9; cut-off distance for coulomb
>> epsilon_r=  1; dielectric constant
>> rvdw=  0.9; cut-off for vdw
>> fourierspacing=  0.12; maximum grid spacing for FFT
>> pme_order=  4; interpolation order for PME
>> ewald_rtol=  1e-5; relative strength of Ewald-shifted
>> DispCorr=  EnerPres ; long range dispersion
>> corrections
>> ;
>> ;Temperature Coupling
>> Tcoupl=  no; type of temperature coupling
>> ;
>> ;Pressure Coupling
>> Pcoupl=  no ; type of pressure coupling
>> ;
>> ;Velocity Generation
>> gen_vel=  no ; generate initial velocities
>> ;
>> ;Bonds
>> constraints=  none; bond constraint type
>>
>> I used gmx solvate to add water molecules to the system.
>>
>> How could I get rid of bad contacts of water molecules? Appreciate if
>> anyone help me to solve the problem.
>>
>
> mdrun stopped after 2000 steps because you told it to. You need to
> minimize further, so increase nsteps (or set it to -1 to let mdrun go as
> long as it needs to without having to guess a number).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
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> 

Re: [gmx-users] Energy Minimization Error

[Justin Lemkul]

On 10/19/17 8:10 PM, Amali Guruge wrote:

Dear Gromacs Users,

I tried to energy minimize my system using the steep integrator. However,
it gave the following message.

Steepest Descents:
Tolerance (Fmax)   =  5.0e+02
Number of steps= 2000
Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06, atom=
14611
Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05, atom=
18527
Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05, atom=
1005
Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
6994
Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
58902
Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
515
Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
188631
Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
188631
Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
188631
Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
188631
Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
188631

step 11: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

After 2000 steps it says,

Steepest Descents did not converge to Fmax < 500 in 2001 steps.
Potential Energy  = -4.6310655e+06
Maximum force =  6.7453154e+03 on atom 18769
Norm of force =  3.3632809e+01

Simulation ended prematurely, no performance report will be written.


my em.mdp file contains following parameters.

integrator=  steep; simulation algorithm
dt=  0.002; time step (ps)
nsteps=  2000; # steps
comm_mode=  linear; c.o.m. motion reset
;
;Energy Minimization
emtol=  500; converged F lt value (kJ mol-1 nm-1)
emstep=  0.01 ; initial step size (nm)
;
;Output Control
nstxout=  5 ; write coordinates to .trr
nstvout=  5; write velocities to .trr
nstlog=  5; write energies to .log
nstenergy=  1; write energies to .edr
;
;Neightbour Searching
cutoff-scheme   =  Verlet; scheme used for
generating pair list
nstlist =  10   ; update neighbour list
ns_type=  grid; neighbour list method
pbc=  xyz; periodic boundary conditions
rlist=  0.9 ; cut-off for short-range neighbour (nm)
;
;Electrostatics and VdW
coulombtype=  PME; type of coulomb interaction
rcoulomb=  0.9; cut-off distance for coulomb
epsilon_r=  1; dielectric constant
rvdw=  0.9; cut-off for vdw
fourierspacing=  0.12; maximum grid spacing for FFT
pme_order=  4; interpolation order for PME
ewald_rtol=  1e-5; relative strength of Ewald-shifted
DispCorr=  EnerPres ; long range dispersion
corrections
;
;Temperature Coupling
Tcoupl=  no; type of temperature coupling
;
;Pressure Coupling
Pcoupl=  no ; type of pressure coupling
;
;Velocity Generation
gen_vel=  no ; generate initial velocities
;
;Bonds
constraints=  none; bond constraint type

I used gmx solvate to add water molecules to the system.

How could I get rid of bad contacts of water molecules? Appreciate if
anyone help me to solve the problem.


mdrun stopped after 2000 steps because you told it to. You need to 
minimize further, so increase nsteps (or set it to -1 to let mdrun go as 
long as it needs to without having to guess a number).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Energy minimization issue

[Justin Lemkul]

On 10/16/17 5:19 AM, Khadija Amine wrote:

Dear Gromacs users,

I'm simulation a double chain protein-ligand complex using Amber force
field. I have written parameters and generated the topology.

The energy minimization of the complex gives me the following error:

*Energy minimization has stopped, but the forces have not converged to the*

*requested precision Fmax < 1000 (which may not be possible for your
system).*

*It stopped because the algorithm tried to make a new step whose size was
too*

*small, or there was no change in the energy since last step. Either way,
we*

*regard the minimization as converged to within the available machine*

*precision, given your starting configuration and EM parameters*

*Double precision normally gives you higher accuracy, but this is often not*

*needed for preparing to run molecular dynamics.*

*You might need to increase your constraint accuracy, or turn*

*off constraints altogether (set constraints = none in mdp file)*
Could you please tell me what is the issue and provide some suggestions


http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] ENERGY MINIMIZATION

[Mark Abraham]

Hi,

In a cygwin terminal, having source'd GMXRC (see the install guide), just
like you need to do under Linux.

Mark

On Tue, Jan 10, 2017 at 7:29 PM Subashini .K  wrote:

> Hi Gromacs users,
>
>
> I have installed gromacs in windows 7, 64 bit using cgywin.
>
>
> I want to use the em.mdp file to grompp and generate a .tpr file.
>
>
> In which terminal should the following commands be executed?
>
>
> ; to test
> ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
> ; mdrun -v -deffnm em
>
> Can someone tell me?
>
>
> Thanks,
>
> Subashini.K
>
>
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Re: [gmx-users] Energy minimization steps

[Syed Azeem]

Thank you Alex and Mark for your replies. :-)

Azeem

> Hi,
>
> How many steps does it take you to walk down a mountain to a certain
> village? :-) Depends where you are on the mountain, and what's in the way.
> But if all you need is to be somewhere near the valley floor to start
> equilibration, anything goes!
>
> Mark
>
> On Wed, 21 Dec 2016 17:11 Alex  wrote:
>
>> This isn't a Gromacs-specific parameter, or, for that matter, anything
>> that straightforwardly depends on the nature of the system
>> (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial
>> cases. The max number of minimization steps is something that limits an
>> energy minimization attempt, given the minimization algorithm,
>> tolerance, the energy step, and, of course, how well-behaved you expect
>> your system to be. It is a reasonable trial and error guess aimed at
>> computational efficiency, e.g. not exceeding a certain amount of
>> computational burden for really bad structures. Alternatively, limiting
>> the number of minimization steps can help not produce some kind of a
>> freaky structure when you have several local minima nearby.
>>
>>
>> Alex
>>
>>
>> On 12/20/2016 10:51 PM, Syed Azeem wrote:
>> > Hi all,
>> >
>> > What is the basis of inputting the maximum number of energy
>> > minimization steps in GROMACS?
>> > Does maximum number of energy minimization steps depend on the number
>> > of residues?
>> >
>> > I came across many articles wherein the authors have described the
>> > number of energy minimization steps within which they have minimized
>> > their protein.
>> >
>> > I have a protein of 596 residues to be simulated.
>> >
>> > Thanks in advance
>> >
>> > Azeem
>>
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Re: [gmx-users] Energy minimization steps

[Mark Abraham]

Hi,

How many steps does it take you to walk down a mountain to a certain
village? :-) Depends where you are on the mountain, and what's in the way.
But if all you need is to be somewhere near the valley floor to start
equilibration, anything goes!

Mark

On Wed, 21 Dec 2016 17:11 Alex  wrote:

> This isn't a Gromacs-specific parameter, or, for that matter, anything
> that straightforwardly depends on the nature of the system
> (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial
> cases. The max number of minimization steps is something that limits an
> energy minimization attempt, given the minimization algorithm,
> tolerance, the energy step, and, of course, how well-behaved you expect
> your system to be. It is a reasonable trial and error guess aimed at
> computational efficiency, e.g. not exceeding a certain amount of
> computational burden for really bad structures. Alternatively, limiting
> the number of minimization steps can help not produce some kind of a
> freaky structure when you have several local minima nearby.
>
>
> Alex
>
>
> On 12/20/2016 10:51 PM, Syed Azeem wrote:
> > Hi all,
> >
> > What is the basis of inputting the maximum number of energy
> > minimization steps in GROMACS?
> > Does maximum number of energy minimization steps depend on the number
> > of residues?
> >
> > I came across many articles wherein the authors have described the
> > number of energy minimization steps within which they have minimized
> > their protein.
> >
> > I have a protein of 596 residues to be simulated.
> >
> > Thanks in advance
> >
> > Azeem
>
> --
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Re: [gmx-users] Energy minimization steps

[Alex]

This isn't a Gromacs-specific parameter, or, for that matter, anything 
that straightforwardly depends on the nature of the system 
(solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial 
cases. The max number of minimization steps is something that limits an 
energy minimization attempt, given the minimization algorithm, 
tolerance, the energy step, and, of course, how well-behaved you expect 
your system to be. It is a reasonable trial and error guess aimed at 
computational efficiency, e.g. not exceeding a certain amount of 
computational burden for really bad structures. Alternatively, limiting 
the number of minimization steps can help not produce some kind of a 
freaky structure when you have several local minima nearby.



Alex


On 12/20/2016 10:51 PM, Syed Azeem wrote:

Hi all,

What is the basis of inputting the maximum number of energy
minimization steps in GROMACS?
Does maximum number of energy minimization steps depend on the number
of residues?

I came across many articles wherein the authors have described the
number of energy minimization steps within which they have minimized
their protein.

I have a protein of 596 residues to be simulated.

Thanks in advance

Azeem


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Re: [gmx-users] Energy Minimization

[Justin Lemkul]

On 11/3/16 10:11 AM, Mishelle Oña wrote:

Positive values of potential energy and I am in vacuo.


Your outcome is exactly what you should expect.  Energies can be positive, and 
almost always are when doing work in vacuo.  The net negative energy in 
condensed phase is driven by attractive solute-solvent and solvent-solvent 
interactions, of which you have none in the gas phase.


-Justin


Mishelle



Sent from my Samsung device


 Original message 
From: Justin Lemkul <jalem...@vt.edu>
Date: 11/03/2016 08:43 (GMT-05:00)
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Energy Minimization



On 11/2/16 9:40 PM, Mishelle Oña wrote:

Hello

I have a question about energy minimization tool. I am modelling a polymer and 
I use a force field I have developed. I have run a EM and got positive values. 
Can you help me with this?



Positive values for what?  Are you in vacuo or in solvent?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy Minimization

[Mishelle Oña]

Positive values of potential energy and I am in vacuo.
Mishelle



Sent from my Samsung device


 Original message 
From: Justin Lemkul <jalem...@vt.edu>
Date: 11/03/2016 08:43 (GMT-05:00)
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Energy Minimization



On 11/2/16 9:40 PM, Mishelle Oña wrote:
> Hello
>
> I have a question about energy minimization tool. I am modelling a polymer 
> and I use a force field I have developed. I have run a EM and got positive 
> values. Can you help me with this?
>

Positive values for what?  Are you in vacuo or in solvent?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy Minimization

[Justin Lemkul]

On 11/2/16 9:40 PM, Mishelle Oña wrote:

Hello

I have a question about energy minimization tool. I am modelling a polymer and 
I use a force field I have developed. I have run a EM and got positive values. 
Can you help me with this?



Positive values for what?  Are you in vacuo or in solvent?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization

[Catarina A. Carvalheda dos Santos]

Hi Surya,

I'm not sure I understand what you want to do.
Do you want to energy minimise an entire trajectory? After the production
phase? Why?

The -c flag in mdrun is the output, the last conformation sampled during
the mdrun. You can use this output file as the input structure for an
energy minimisation (-c option in grompp to prepare the .tpr file), I just
don't see the point in doing that.
Also, -c flag in grompp doesn't accept .xtc files. If you type "grompp -h"
you'll see that.

Cheers,


On 28 September 2016 at 05:53, Seera Suryanarayana 
wrote:

> Dear gromacs users,
> I have done simulations for 100ns. I would like to do energy minimization
> by using trajectory file which I got after production phase. Can I do
> energy minimization passing the trajectory file to -c argument? If it is
> yes, then tell me how to do it.
>
> Thanks in advance
>
> Surya
> Graduate student
> India.
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>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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Re: [gmx-users] Energy minimization has stopped

[Anurag Dobhal]

Thanks a lot Justinn and Mark for the valuable suggestions.

I will start over again by choosing a force field which is suitable for the
RNA molecules.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:55 PM, Justin Lemkul  wrote:

>
>
> On 6/23/16 7:17 AM, Anurag Dobhal wrote:
>
>> Dear Justin,
>>
>> The main aim of the study is to study the interaction between a polymer
>> (chitosan) and RNA molecules by simulating them togather. I have already
>> successfully simulated my polymer system using OPLS AA force field.
>>
>> To simulate them together I need to write the OPLS AA parameters for RNA
>> molecules. I was suggested (Link Below) earlier that I can take the
>> charges
>> from any other forcefield.
>>
>> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)
>>
>> please enlight me where I am going wrong.
>>
>>
> I think you misunderstood what I said in that thread.
>
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html
>
> "You should find force field parameters specifically for the base from
> published literature or from another force field."
>
> This means: find a force field that has parametrized the species you need
> and use it.  This does not mean: hack together something from "any other
> force field" you like and try to make it OPLS-AA.  You did not say before
> that you were dealing with a complex system like this.  You just said your
> guanine charges didn't add up.  So I addressed that problem.
>
> Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an
> invalid approach.
>
> Pick a force field.  Use that force field.  Do not try to kludge together
> some hybrid entity.  Force fields are designed to be internally
> self-consistent.  If you do not have a proper balance of interactions, you
> are not doing a useful simulation.  You are generating random numbers.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
>
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Re: [gmx-users] Energy minimization has stopped

[Justin Lemkul]

On 6/23/16 7:17 AM, Anurag Dobhal wrote:

Dear Justin,

The main aim of the study is to study the interaction between a polymer
(chitosan) and RNA molecules by simulating them togather. I have already
successfully simulated my polymer system using OPLS AA force field.

To simulate them together I need to write the OPLS AA parameters for RNA
molecules. I was suggested (Link Below) earlier that I can take the charges
from any other forcefield.

(http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)

please enlight me where I am going wrong.



I think you misunderstood what I said in that thread.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html

"You should find force field parameters specifically for the base from published 
literature or from another force field."


This means: find a force field that has parametrized the species you need and 
use it.  This does not mean: hack together something from "any other force 
field" you like and try to make it OPLS-AA.  You did not say before that you 
were dealing with a complex system like this.  You just said your guanine 
charges didn't add up.  So I addressed that problem.


Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an 
invalid approach.


Pick a force field.  Use that force field.  Do not try to kludge together some 
hybrid entity.  Force fields are designed to be internally self-consistent.  If 
you do not have a proper balance of interactions, you are not doing a useful 
simulation.  You are generating random numbers.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization has stopped

[Mark Abraham]

Hi,

You were recommended to pick a force field, not to combine parts of force
fields. Choosing to simulate your polymer OPLS/AA if you then want to
combine with RNA is not a good experimental design, unless you can do the
combined simulation also in OPLS/AA. I would repeat the polymer experiment
in whatever forcefield is also good for the experiment with RNA.

Mark

On Thu, Jun 23, 2016 at 1:18 PM Anurag Dobhal <
anurag.dob...@nano-medicine.co.in> wrote:

> Dear Justin,
>
> The main aim of the study is to study the interaction between a polymer
> (chitosan) and RNA molecules by simulating them togather. I have already
> successfully simulated my polymer system using OPLS AA force field.
>
> To simulate them together I need to write the OPLS AA parameters for RNA
> molecules. I was suggested (Link Below) earlier that I can take the charges
> from any other forcefield.
>
> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)
>
> please enlight me where I am going wrong.
>
> Thank You
>
>
>
>
>
>
>
>
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
> *Institute of Chemical Technology, Mumbai*
> *Contact: +91 8898486877*
>
>
> On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 6/23/16 7:00 AM, Anurag Dobhal wrote:
> >
> >> I am using OPLS AA force field. parameters (charges) for the atoms are
> >> taken from the charmm27 force field.
> >>
> >>
> > So, by using some hybridized force field, you can't successfully minimize
> > a structure.  That should tell you something.  Why are you trying to do
> > this, and what leads you to believe that some hybrid OPLS/CHARMM
> > combination is even sensible?  You can't just mix the charges from one
> > force field with another to create some kind of Frankenforcefield.
> >
> > Recent RNA force fields like CHARMM36 and recent AMBER updates are highly
> > optimized for RNA simulations.
> >
> > -Justin
> >
> >
> >>
> >>
> >> *Anurag Dobhal*
> >> *Graduate Student (Bioprocess Technology)*
> >> *Institute of Chemical Technology, Mumbai*
> >> *Contact: +91 8898486877*
> >>
> >>
> >>
> >> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:
> >>
> >>
> >>>
> >>> On 6/23/16 6:44 AM, Justin Lemkul wrote:
> >>>
> >>>
> 
>  On 6/23/16 6:35 AM, Anurag Dobhal wrote:
> 
>  Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA
> force
> > field. I have written parameters using CHARMM27 force field for RNA
> > molecules.
> >
> >
> > What does this mean?  Are you using OPLS-AA or CHARMM27?
> 
> 
>  Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
> >>> superior for RNA.
> >>>
> >>> -Justin
> >>>
> >>>
> >>> Minimising the molecule by invoking mdrun gives me the follwoing error.
> >>>
> 
> > Energy minimization has stopped, but the forces have not converged to
> > the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size
> > was
> > too
> > small, or there was no change in the energy since last step. Either
> > way,
> > we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is
> often
> > not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> >
> >
> >
> -
> >
> > The contents of the .mdp file are the following
> >
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > integrator = steep ; Algorithm (steep = steepest descent
> minimization)
> > emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
> > kJ/mol/nm
> > emstep  = 0.01  ; Energy step size
> > nsteps = 5   ; Maximum number of (minimization) steps to perform
> >
> > ; Parameters describing how to find the neighbors of each atom and
> how
> > to
> > calculate the interactions
> > nstlist= 1; Frequency to update the neighbor list and long
> > range
> > forces
> > cutoff-scheme   = Verlet
> > ns_type= grid ; Method to determine neighbor list (simple, grid)
> > coulombtype= PME ; Treatment of long range electrostatic
> > interactions
> > rcoulomb= 1.0 ; Short-range electrostatic cut-off
> > rvdw= 1.0 ; Short-range Van der Waals cut-off
> > pbc= xyz ; Periodic Boundary Conditions (yes/no)
> >
> > any suggestions ?
> >
> >
> >
> 
> 
> 

Re: [gmx-users] Energy minimization has stopped

[Anurag Dobhal]

Dear Justin,

The main aim of the study is to study the interaction between a polymer
(chitosan) and RNA molecules by simulating them togather. I have already
successfully simulated my polymer system using OPLS AA force field.

To simulate them together I need to write the OPLS AA parameters for RNA
molecules. I was suggested (Link Below) earlier that I can take the charges
from any other forcefield.

(http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)

please enlight me where I am going wrong.

Thank You








*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul  wrote:

>
>
> On 6/23/16 7:00 AM, Anurag Dobhal wrote:
>
>> I am using OPLS AA force field. parameters (charges) for the atoms are
>> taken from the charmm27 force field.
>>
>>
> So, by using some hybridized force field, you can't successfully minimize
> a structure.  That should tell you something.  Why are you trying to do
> this, and what leads you to believe that some hybrid OPLS/CHARMM
> combination is even sensible?  You can't just mix the charges from one
> force field with another to create some kind of Frankenforcefield.
>
> Recent RNA force fields like CHARMM36 and recent AMBER updates are highly
> optimized for RNA simulations.
>
> -Justin
>
>
>>
>>
>> *Anurag Dobhal*
>> *Graduate Student (Bioprocess Technology)*
>> *Institute of Chemical Technology, Mumbai*
>> *Contact: +91 8898486877*
>>
>>
>>
>> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 6/23/16 6:44 AM, Justin Lemkul wrote:
>>>
>>>

 On 6/23/16 6:35 AM, Anurag Dobhal wrote:

 Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
> field. I have written parameters using CHARMM27 force field for RNA
> molecules.
>
>
> What does this mean?  Are you using OPLS-AA or CHARMM27?


 Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
>>> superior for RNA.
>>>
>>> -Justin
>>>
>>>
>>> Minimising the molecule by invoking mdrun gives me the follwoing error.
>>>

> Energy minimization has stopped, but the forces have not converged to
> the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size
> was
> too
> small, or there was no change in the energy since last step. Either
> way,
> we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often
> not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
>
>
> -
>
> The contents of the .mdp file are the following
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
> kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps = 5   ; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how
> to
> calculate the interactions
> nstlist= 1; Frequency to update the neighbor list and long
> range
> forces
> cutoff-scheme   = Verlet
> ns_type= grid ; Method to determine neighbor list (simple, grid)
> coulombtype= PME ; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.0 ; Short-range electrostatic cut-off
> rvdw= 1.0 ; Short-range Van der Waals cut-off
> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>
> any suggestions ?
>
>
>

 http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision


 mdrun prints which atom is feeling the maximum force, so that's a good
 place to
 start looking to see if there is an actual problem.

 -Justin


 --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> 

Re: [gmx-users] Energy minimization has stopped

[Justin Lemkul]

On 6/23/16 7:00 AM, Anurag Dobhal wrote:

I am using OPLS AA force field. parameters (charges) for the atoms are
taken from the charmm27 force field.



So, by using some hybridized force field, you can't successfully minimize a 
structure.  That should tell you something.  Why are you trying to do this, and 
what leads you to believe that some hybrid OPLS/CHARMM combination is even 
sensible?  You can't just mix the charges from one force field with another to 
create some kind of Frankenforcefield.


Recent RNA force fields like CHARMM36 and recent AMBER updates are highly 
optimized for RNA simulations.


-Justin





*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:




On 6/23/16 6:44 AM, Justin Lemkul wrote:




On 6/23/16 6:35 AM, Anurag Dobhal wrote:


Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.



What does this mean?  Are you using OPLS-AA or CHARMM27?



Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
superior for RNA.

-Justin


Minimising the molecule by invoking mdrun gives me the follwoing error.


Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your
system).
It stopped because the algorithm tried to make a new step whose size was
too
small, or there was no change in the energy since last step. Either way,
we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often
not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)


-

The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?




http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision


mdrun prints which atom is feeling the maximum force, so that's a good
place to
start looking to see if there is an actual problem.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at
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posting!

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* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.





--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Energy minimization has stopped

[Anurag Dobhal]

I am using OPLS AA force field. parameters (charges) for the atoms are
taken from the charmm27 force field.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:

>
>
> On 6/23/16 6:44 AM, Justin Lemkul wrote:
>
>>
>>
>> On 6/23/16 6:35 AM, Anurag Dobhal wrote:
>>
>>> Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
>>> field. I have written parameters using CHARMM27 force field for RNA
>>> molecules.
>>>
>>>
>> What does this mean?  Are you using OPLS-AA or CHARMM27?
>>
>>
> Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
> superior for RNA.
>
> -Justin
>
>
> Minimising the molecule by invoking mdrun gives me the follwoing error.
>>>
>>> Energy minimization has stopped, but the forces have not converged to the
>>> requested precision Fmax < 1000 (which may not be possible for your
>>> system).
>>> It stopped because the algorithm tried to make a new step whose size was
>>> too
>>> small, or there was no change in the energy since last step. Either way,
>>> we
>>> regard the minimization as converged to within the available machine
>>> precision, given your starting configuration and EM parameters.
>>>
>>> Double precision normally gives you higher accuracy, but this is often
>>> not
>>> needed for preparing to run molecular dynamics.
>>> You might need to increase your constraint accuracy, or turn
>>> off constraints altogether (set constraints = none in mdp file)
>>>
>>>
>>> -
>>>
>>> The contents of the .mdp file are the following
>>>
>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>> integrator = steep ; Algorithm (steep = steepest descent minimization)
>>> emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
>>> kJ/mol/nm
>>> emstep  = 0.01  ; Energy step size
>>> nsteps = 5   ; Maximum number of (minimization) steps to perform
>>>
>>> ; Parameters describing how to find the neighbors of each atom and how to
>>> calculate the interactions
>>> nstlist= 1; Frequency to update the neighbor list and long range
>>> forces
>>> cutoff-scheme   = Verlet
>>> ns_type= grid ; Method to determine neighbor list (simple, grid)
>>> coulombtype= PME ; Treatment of long range electrostatic interactions
>>> rcoulomb= 1.0 ; Short-range electrostatic cut-off
>>> rvdw= 1.0 ; Short-range Van der Waals cut-off
>>> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>>>
>>> any suggestions ?
>>>
>>>
>>
>> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
>>
>>
>> mdrun prints which atom is feeling the maximum force, so that's a good
>> place to
>> start looking to see if there is an actual problem.
>>
>> -Justin
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Energy minimization has stopped

[Justin Lemkul]

On 6/23/16 6:44 AM, Justin Lemkul wrote:



On 6/23/16 6:35 AM, Anurag Dobhal wrote:

Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.



What does this mean?  Are you using OPLS-AA or CHARMM27?



Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly superior 
for RNA.


-Justin


Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

-

The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?



http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision


mdrun prints which atom is feeling the maximum force, so that's a good place to
start looking to see if there is an actual problem.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization has stopped

[Justin Lemkul]

On 6/23/16 6:35 AM, Anurag Dobhal wrote:

Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.



What does this mean?  Are you using OPLS-AA or CHARMM27?


Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

-
The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?



http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

mdrun prints which atom is feeling the maximum force, so that's a good place to 
start looking to see if there is an actual problem.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization error

[faride badalkhani]

Hi,

Thanks a lot for your time and patience. This time, I chose a very simple
structure and then inspected the generated topology. The interesting point
was that, there were some missing interactions. When I inspected them. I
found that I had defined those interactions in ffbonded.itp file, but
pdb2gmx has not assigned those definitions to these interactions. However,
I added the appropriate gb_, ga_, or gd_ manually, and then performed the
MD simulations and received an error as follows:

Step=  210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom= 46
Step=  212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom= 44
Step=  216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom= 46
Step=  218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom= 44
Step=  221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom= 46
Step=  224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom= 44
Step=  227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom= 46
Step=  229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom= 44
Step=  232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom= 46
Step=  234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom= 44
Step=  235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom= 46
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 236 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -8.9157188e+04
Maximum force =  1.7089320e+05 on atom 44
Norm of force =  3.3110510e+03

gcq#220: "Let's Go Hang Out In a Mall" (LIVE)

farideh@farideh-P61A-D3:~/multiple/G0$

you can access all the files via the following link:
https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0

Truly yours,
Farideh

On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham 
wrote:

> Hi,
>
> Did you inspect your topology like I suggested? You need to know that there
> are bonds exactly where you intend them, before doing any calculations with
> them.
>
> Mark
>
> On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Hi,
> >
> > I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
> > But, every time the system blows up at energy minimization step.
> Therefore,
> > according to what Mark had recommended I decided to start with a much
> > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
> > optimized it at M062x/6-31G* level, before starting the MD simulations.
> > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> > residue by residue. After that, I started simulation procedure and
> > continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
> > errors in energy minimization step, and the potential energy - EM step
> plot
> > was reasonable. But, when I loaded em.gro file in VMD, the structure was
> > completely messed up as in G3 dendrimer. This time I continued the MD
> > simulation until production MD, and there was no error. However, the
> system
> > is blown up. You can access all the simulation files, pdb structure, and
> > the photos of G1 structure before and after EM step via:
> >
> > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
> >
> > Since I am a beginner in this area, I do not know what is the solution
> for
> > this problem.
> > Do you think errors that occur during the G3 simulation are relevant to
> the
> > initial structure?
> > any suggestion or recommendation is appreciated.
> >
> > Thanks in advance
> > Farideh
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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>
> * Please search the archive at
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Re: [gmx-users] energy minimization error

[Mark Abraham]

Hi,

pdb2gmx and grompp are pretty talkative about things like missing
parameters and bonds - go back and read what they had to say, and
particularly what pdb2gmx thought about your specbonds.

Mark

On Fri, Oct 23, 2015 at 5:51 PM faride badalkhani 
wrote:

> Hi,
>
> Thanks a lot for your time and patience. This time, I chose a very simple
> structure and then inspected the generated topology. The interesting point
> was that, there were some missing interactions. When I inspected them. I
> found that I had defined those interactions in ffbonded.itp file, but
> pdb2gmx has not assigned those definitions to these interactions. However,
> I added the appropriate gb_, ga_, or gd_ manually, and then performed the
> MD simulations and received an error as follows:
>
> Step=  210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom=
> 46
> Step=  212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom=
> 44
> Step=  216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom=
> 46
> Step=  218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom=
> 44
> Step=  221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom=
> 46
> Step=  224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom=
> 44
> Step=  227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom=
> 46
> Step=  229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom=
> 44
> Step=  232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom=
> 46
> Step=  234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom=
> 44
> Step=  235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom=
> 46
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 100 (which may not be possible for your system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 236 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -8.9157188e+04
> Maximum force =  1.7089320e+05 on atom 44
> Norm of force =  3.3110510e+03
>
> gcq#220: "Let's Go Hang Out In a Mall" (LIVE)
>
> farideh@farideh-P61A-D3:~/multiple/G0$
>
> you can access all the files via the following link:
> https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0
>
> Truly yours,
> Farideh
>
> On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Did you inspect your topology like I suggested? You need to know that
> there
> > are bonds exactly where you intend them, before doing any calculations
> with
> > them.
> >
> > Mark
> >
> > On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani <
> > farideh.kham...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > I am trying to simulate a hyper-branched polymer (a dendrimer) in
> water.
> > > But, every time the system blows up at energy minimization step.
> > Therefore,
> > > according to what Mark had recommended I decided to start with a much
> > > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I
> had
> > > optimized it at M062x/6-31G* level, before starting the MD simulations.
> > > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> > > residue by residue. After that, I started simulation procedure and
> > > continued step by step. In spite of G3 PAMAM dendrimer I didn't face
> any
> > > errors in energy minimization step, and the potential energy - EM step
> > plot
> > > was reasonable. But, when I loaded em.gro file in VMD, the structure
> was
> > > completely messed up as in G3 dendrimer. This time I continued the MD
> > > simulation until production MD, and there was no error. However, the
> > system
> > > is blown up. You can access all the simulation files, pdb structure,
> and
> > > the photos of G1 structure before and after EM step via:
> > >
> > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
> > >
> > > Since I am a beginner in this area, I do not know what is the solution
> > for
> > > this problem.
> > > Do you think errors that occur during the G3 simulation are relevant to
> > the
> > > initial structure?
> > > any suggestion or recommendation is appreciated.
> > >
> > > Thanks in advance
> > > Farideh
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * 

Re: [gmx-users] energy minimization error

[Mark Abraham]

Hi,

Did you inspect your topology like I suggested? You need to know that there
are bonds exactly where you intend them, before doing any calculations with
them.

Mark

On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani 
wrote:

> Hi,
>
> I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
> But, every time the system blows up at energy minimization step. Therefore,
> according to what Mark had recommended I decided to start with a much
> smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
> optimized it at M062x/6-31G* level, before starting the MD simulations.
> Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> residue by residue. After that, I started simulation procedure and
> continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
> errors in energy minimization step, and the potential energy - EM step plot
> was reasonable. But, when I loaded em.gro file in VMD, the structure was
> completely messed up as in G3 dendrimer. This time I continued the MD
> simulation until production MD, and there was no error. However, the system
> is blown up. You can access all the simulation files, pdb structure, and
> the photos of G1 structure before and after EM step via:
>
> https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
>
> Since I am a beginner in this area, I do not know what is the solution for
> this problem.
> Do you think errors that occur during the G3 simulation are relevant to the
> initial structure?
> any suggestion or recommendation is appreciated.
>
> Thanks in advance
> Farideh
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Energy minimization error

[faride badalkhani]

Hi,

As you said, I started with a G1 PAMAM dendrimer, rather than a G3 one. I
had optimized it at M062x/6-31G* level, before starting the MD simulations.
Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
residue by residue. After that, I started simulation procedure and
continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
errors in energy minimization step, and the potential energy - EM step plot
was reasonable. But, when I loaded em.gro file in VMD, the structure was
completely messed up as in G3 dendrimer. This time I continued the MD
simulation until production MD, and there was no error. However, the system
is blown up. You can access all the simulation files, pdb structure, and
the photos of G1 structure before and after EM step via:

https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0

Since I am a beginner in this area, I do not know what is the solution for
this problem.
Do you think errors that occur during the G3 simulation are relevant to the
initial structure?
any suggestion or recommendation is appreciated.

Thanks in advance
Farideh

On Sat, Oct 17, 2015 at 6:29 PM, Mark Abraham 
wrote:

> Hi,
>
> What some visualization program shows about bonds doesn't mean anything -
> it has not parsed your topology. You have no option but to look at the .top
> produced and reason about what it shows, but yours is very complex. I
> strongly recommend starting with something simpler than a multiply branched
> dendrimer. Join two units with a specbond, inspect the .top so that you
> know it has what you think it has, and get that to EM and simulation
> stably. Then you can get more complex.
>
> Mark
>
> On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Dear gromacs users,
> >
> > As I said before I faced with the minimization error, so I changed
> > coordinates of atoms in pdb file, but the problem is the same. the only
> > thing that changes in every run is atom number. I modified pdb for many
> > times.
> >
> > Steepest Descents converged to Fmax < 1000 in 530 steps
> > Potential Energy  = -5.5180181e+05
> > Maximum force =  7.4496063e+02 on atom 501
> > Norm of force =  3.8248455e+01
> >
> >
> > Moreover gro structure was completely messed up when was visualized in
> vmd.
> > you can see the picture of my structure in below dropbox link:
> >
> > https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
> > https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0
> >
> > and this is the pdb file dropbox link:
> >
> > https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0
> >
> >
> > I used cg algorithm after steep for minimization, too. But it did not
> work.
> > is there any way to solve this problem?
> >
> > any help is appreciated.
> >
> > On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Look at atom 380 and see why the forces might be high.
> > >
> > > Mark
> > >
> > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> > > farideh.kham...@gmail.com>
> > > wrote:
> > >
> > > > Thank you for your great help on specbond.dat file. I defined it and
> I
> > > > could go ahead until Energy minimization step. I have used this
> > minim.mdp
> > > > file
> > > >
> > > > ; minim.mdp - used as input into grompp to generate em.tpr
> > > > ; Parameters describing what to do, when to stop and what to save
> > > > integrator= steep; Algorithm (steep = steepest descent
> > > > minimization)
> > > > emtol  = 1000.0  ; Stop minimization when the maximum
> > force <
> > > > 1000.0 kJ/mol/nm
> > > > emstep   = 0.01  ; Energy step size
> > > > nsteps= 5  ; Maximum number of (minimization)
> steps
> > > to
> > > > perform
> > > >
> > > > ; Parameters describing how to find the neighbors of each atom and
> how
> > to
> > > > calculate the interactions
> > > > nstlist  = 1; Frequency to update the neighbor
> list
> > > and
> > > > long range forces
> > > > ns_type   = grid; Method to determine neighbor list
> > > > (simple, grid)
> > > > rlist = 1.0; Cut-off for making neighbor list
> > > > (short range forces)
> > > > coulombtype= PME; Treatment of long range electrostatic
> > > > interactions
> > > > rcoulomb = 1.0; Short-range electrostatic cut-off
> > > > rvdw   = 1.0; Short-range Van der Waals cut-off
> > > > pbc = xyz ; Periodic Boundary Conditions
> > (yes/no)
> > > >
> > > > But when I run mdrun -v -deffnm em command, I get this error:
> > > >
> > > > Energy minimization has stopped, but the forces have not converged to
> > the
> > > > requested precision Fmax < 1000 (which may not be possible for your
> > > > system).
> > > > It stopped because the algorithm tried to make a new step whose size
> > was
> > > > too
> > > > small, or there was no change 

Re: [gmx-users] Energy minimization error

[faride badalkhani]

Dear gromacs users,

As I said before I faced with the minimization error, so I changed
coordinates of atoms in pdb file, but the problem is the same. the only
thing that changes in every run is atom number. I modified pdb for many
times.

Steepest Descents converged to Fmax < 1000 in 530 steps
Potential Energy  = -5.5180181e+05
Maximum force =  7.4496063e+02 on atom 501
Norm of force =  3.8248455e+01


Moreover gro structure was completely messed up when was visualized in vmd.
you can see the picture of my structure in below dropbox link:

https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0

and this is the pdb file dropbox link:

https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0


I used cg algorithm after steep for minimization, too. But it did not work.
is there any way to solve this problem?

any help is appreciated.

On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
wrote:

> Hi,
>
> Look at atom 380 and see why the forces might be high.
>
> Mark
>
> On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Thank you for your great help on specbond.dat file. I defined it and I
> > could go ahead until Energy minimization step. I have used this minim.mdp
> > file
> >
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > ; Parameters describing what to do, when to stop and what to save
> > integrator= steep; Algorithm (steep = steepest descent
> > minimization)
> > emtol  = 1000.0  ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > emstep   = 0.01  ; Energy step size
> > nsteps= 5  ; Maximum number of (minimization) steps
> to
> > perform
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist  = 1; Frequency to update the neighbor list
> and
> > long range forces
> > ns_type   = grid; Method to determine neighbor list
> > (simple, grid)
> > rlist = 1.0; Cut-off for making neighbor list
> > (short range forces)
> > coulombtype= PME; Treatment of long range electrostatic
> > interactions
> > rcoulomb = 1.0; Short-range electrostatic cut-off
> > rvdw   = 1.0; Short-range Van der Waals cut-off
> > pbc = xyz ; Periodic Boundary Conditions (yes/no)
> >
> > But when I run mdrun -v -deffnm em command, I get this error:
> >
> > Energy minimization has stopped, but the forces have not converged to the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size was
> > too
> > small, or there was no change in the energy since last step. Either way,
> we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is often
> not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to machine precision in 90 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy  = -2.3956744e+05
> > Maximum force =  1.5824519e+05 on atom 380
> > Norm of force =  1.7695243e+03
> >
> > gcq#187: "Been There, Done It" (Beavis and Butthead)
> >
> > farideh@farideh-P61A-D3:~/FARIDEH$
> >
> > I changed the emtol, emstep, and nsteps for a few times. However, I
> > couldn't resolve this problem. Could you tell me if there is something
> > wrong with the minim.mdp file?
> >
> > You can see all the files via:
> > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
> >
> > Truly yours,
> > Farideh
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] Energy minimization error

[Mark Abraham]

Hi,

What some visualization program shows about bonds doesn't mean anything -
it has not parsed your topology. You have no option but to look at the .top
produced and reason about what it shows, but yours is very complex. I
strongly recommend starting with something simpler than a multiply branched
dendrimer. Join two units with a specbond, inspect the .top so that you
know it has what you think it has, and get that to EM and simulation
stably. Then you can get more complex.

Mark

On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani 
wrote:

> Dear gromacs users,
>
> As I said before I faced with the minimization error, so I changed
> coordinates of atoms in pdb file, but the problem is the same. the only
> thing that changes in every run is atom number. I modified pdb for many
> times.
>
> Steepest Descents converged to Fmax < 1000 in 530 steps
> Potential Energy  = -5.5180181e+05
> Maximum force =  7.4496063e+02 on atom 501
> Norm of force =  3.8248455e+01
>
>
> Moreover gro structure was completely messed up when was visualized in vmd.
> you can see the picture of my structure in below dropbox link:
>
> https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
> https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0
>
> and this is the pdb file dropbox link:
>
> https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0
>
>
> I used cg algorithm after steep for minimization, too. But it did not work.
> is there any way to solve this problem?
>
> any help is appreciated.
>
> On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Look at atom 380 and see why the forces might be high.
> >
> > Mark
> >
> > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> > farideh.kham...@gmail.com>
> > wrote:
> >
> > > Thank you for your great help on specbond.dat file. I defined it and I
> > > could go ahead until Energy minimization step. I have used this
> minim.mdp
> > > file
> > >
> > > ; minim.mdp - used as input into grompp to generate em.tpr
> > > ; Parameters describing what to do, when to stop and what to save
> > > integrator= steep; Algorithm (steep = steepest descent
> > > minimization)
> > > emtol  = 1000.0  ; Stop minimization when the maximum
> force <
> > > 1000.0 kJ/mol/nm
> > > emstep   = 0.01  ; Energy step size
> > > nsteps= 5  ; Maximum number of (minimization) steps
> > to
> > > perform
> > >
> > > ; Parameters describing how to find the neighbors of each atom and how
> to
> > > calculate the interactions
> > > nstlist  = 1; Frequency to update the neighbor list
> > and
> > > long range forces
> > > ns_type   = grid; Method to determine neighbor list
> > > (simple, grid)
> > > rlist = 1.0; Cut-off for making neighbor list
> > > (short range forces)
> > > coulombtype= PME; Treatment of long range electrostatic
> > > interactions
> > > rcoulomb = 1.0; Short-range electrostatic cut-off
> > > rvdw   = 1.0; Short-range Van der Waals cut-off
> > > pbc = xyz ; Periodic Boundary Conditions
> (yes/no)
> > >
> > > But when I run mdrun -v -deffnm em command, I get this error:
> > >
> > > Energy minimization has stopped, but the forces have not converged to
> the
> > > requested precision Fmax < 1000 (which may not be possible for your
> > > system).
> > > It stopped because the algorithm tried to make a new step whose size
> was
> > > too
> > > small, or there was no change in the energy since last step. Either
> way,
> > we
> > > regard the minimization as converged to within the available machine
> > > precision, given your starting configuration and EM parameters.
> > >
> > > Double precision normally gives you higher accuracy, but this is often
> > not
> > > needed for preparing to run molecular dynamics.
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints altogether (set constraints = none in mdp file)
> > >
> > > writing lowest energy coordinates.
> > >
> > > Steepest Descents converged to machine precision in 90 steps,
> > > but did not reach the requested Fmax < 1000.
> > > Potential Energy  = -2.3956744e+05
> > > Maximum force =  1.5824519e+05 on atom 380
> > > Norm of force =  1.7695243e+03
> > >
> > > gcq#187: "Been There, Done It" (Beavis and Butthead)
> > >
> > > farideh@farideh-P61A-D3:~/FARIDEH$
> > >
> > > I changed the emtol, emstep, and nsteps for a few times. However, I
> > > couldn't resolve this problem. Could you tell me if there is something
> > > wrong with the minim.mdp file?
> > >
> > > You can see all the files via:
> > > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
> > >
> > > Truly yours,
> > > Farideh
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > 

Re: [gmx-users] Energy minimization error

[Mark Abraham]

Hi,

Look at atom 380 and see why the forces might be high.

Mark

On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani 
wrote:

> Thank you for your great help on specbond.dat file. I defined it and I
> could go ahead until Energy minimization step. I have used this minim.mdp
> file
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator= steep; Algorithm (steep = steepest descent
> minimization)
> emtol  = 1000.0  ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep   = 0.01  ; Energy step size
> nsteps= 5  ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist  = 1; Frequency to update the neighbor list and
> long range forces
> ns_type   = grid; Method to determine neighbor list
> (simple, grid)
> rlist = 1.0; Cut-off for making neighbor list
> (short range forces)
> coulombtype= PME; Treatment of long range electrostatic
> interactions
> rcoulomb = 1.0; Short-range electrostatic cut-off
> rvdw   = 1.0; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>
> But when I run mdrun -v -deffnm em command, I get this error:
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 90 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -2.3956744e+05
> Maximum force =  1.5824519e+05 on atom 380
> Norm of force =  1.7695243e+03
>
> gcq#187: "Been There, Done It" (Beavis and Butthead)
>
> farideh@farideh-P61A-D3:~/FARIDEH$
>
> I changed the emtol, emstep, and nsteps for a few times. However, I
> couldn't resolve this problem. Could you tell me if there is something
> wrong with the minim.mdp file?
>
> You can see all the files via:
> https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
>
> Truly yours,
> Farideh
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Energy minimization

[Justin Lemkul]

On 7/8/15 8:03 PM, Malihe Hasanzadeh wrote:

Hi,
I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I
do energy minimization, my system is converged but has positive potential
energy. also this step only takes 3 second! for next step (pr), gives error:
your system is not equilibrated well and blowing up! I chcked my em.pdb
file and
I saw the Sol box is separated from protein and DNA!


This is probably just a PBC effect; use trjconv.


Could you please help me, what should I do?what part of my set is wrong?



Your EM outcome suggests an unresolvable clash in the system, so it's pointless 
to try dynamics unless you get a force below the specified tolerance (or at 
least of some other reasonable magnitude).  mdrun tells you where the maximum 
force is, so that's where you should start looking.  Beyond that, you'll have to 
give us a complete description of what you've done to prepare the system, 
parametrize the ligand, etc.  General troubleshooting that you should always follow:


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System


my em.mdp:
define = -DFLEXIBLE


I'm assuming you're trying to use rigid water during the subsequent dynamics 
(you should), so you'll want to re-minimize without flexible water. 
Occasionally, the waters distort and SETTLE cannot fix the geometry.  This is 
not likely the source of your problem, just an FYI.


-Justin


integrator = cg ; steep
nsteps = 4000
nstlist = 1
constraints = none
emtol = 100.0
nstcgsteep = 10 ; do a steep every 10 steps of cg
emstep = 0.01 ; used with steep
nstcomm = 1
nstcalcenergy = 1.2
ewald_rtol = 1e-05
coulombtype = PME
cutoff-scheme = Group
ns_type = grid
rlist = 1.4
rcoulomb =1.4
rvdw = 1.4
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 0 ; write coords every # step
optimize_fft = yes

Sincerely,
Malihe



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization error

[James Lord]

Hi Justin
For now I  used


*mdrun -nt 1*


* and got rid of this error so hopefully the simulation wont crash. *

*Cheers*

*James*


On Sat, Jun 27, 2015 at 11:19 AM, James Lord jjamesgreen...@gmail.com
wrote:

 Hi Justin,
 I have asked this before, but this time I started up from scratch and used
 the input files that I know they are fine but again I am getting this
 error, Would you please tell me what is wrong in my topology files and
 where about in .top files the bond length are defined?


 https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing

 Cheers
 James

 On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/16/15 11:35 PM, James Lord wrote:

 Hi Justin
 Thanks for this. Can you tell me which step(s) this bond length is
 defined
 What should I do (redo) to resolve this issue?


 The bonds are defined in the topology.  The DD algorithm reads what's in
 the coordinate file and builds cells based on the geometry it finds there.

 Without a full description of what's in your system, what steps you've
 taken to prepare it (full commands, in order), there's little I can suggest
 because it would all be guesswork.


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.



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Re: [gmx-users] energy minimization error

[Justin Lemkul]

On 6/27/15 2:29 AM, James Lord wrote:

Hi Justin
For now I  used


*mdrun -nt 1*


* and got rid of this error so hopefully the simulation wont crash. *



The DD errors have nothing to do with physical stability; you just can't 
necessarily parallelize any arbitrary system over any arbitrary number of cores 
(DD cells).  You can also parallelize with OpenMP to get some speed-up (mdrun 
-ntmpi 1 -ntomp N).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization error

[Justin Lemkul]

On 6/26/15 7:19 PM, James Lord wrote:

Hi Justin,
I have asked this before, but this time I started up from scratch and used
the input files that I know they are fine but again I am getting this
error, Would you please tell me what is wrong in my topology files and
where about in .top files the bond length are defined?

https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing



There's nothing I can do with a topology that's a series of #include statements.

Please also remind me what this is all about so I don't have to go digging 
through the archives for something from a month ago.  Lots of things have 
happened since then :)


-Justin


Cheers
James

On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:




On 5/16/15 11:35 PM, James Lord wrote:


Hi Justin
Thanks for this. Can you tell me which step(s) this bond length is
defined
What should I do (redo) to resolve this issue?



The bonds are defined in the topology.  The DD algorithm reads what's in
the coordinate file and builds cells based on the geometry it finds there.

Without a full description of what's in your system, what steps you've
taken to prepare it (full commands, in order), there's little I can suggest
because it would all be guesswork.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization error

[James Lord]

Hi Justin,
I have asked this before, but this time I started up from scratch and used
the input files that I know they are fine but again I am getting this
error, Would you please tell me what is wrong in my topology files and
where about in .top files the bond length are defined?

https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing

Cheers
James

On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/16/15 11:35 PM, James Lord wrote:

 Hi Justin
 Thanks for this. Can you tell me which step(s) this bond length is
 defined
 What should I do (redo) to resolve this issue?


 The bonds are defined in the topology.  The DD algorithm reads what's in
 the coordinate file and builds cells based on the geometry it finds there.

 Without a full description of what's in your system, what steps you've
 taken to prepare it (full commands, in order), there's little I can suggest
 because it would all be guesswork.


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Re: [gmx-users] energy minimization problem

[Justin Lemkul]

On 6/1/15 8:06 AM, soumadwip ghosh wrote:

Thanks Justin for your quick reply. What are the correct non-bonding
settings for CHARMM to be used in the .mdp file?



http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

I seem to have to post this information weekly...


Here is how the CNT molecule looks like prior to energy minimization.

pre energy min CNT
https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing



Yep, that's definitely wrong.


I am not continuing any of the equilibration steps anymore. As you can see
the CNT structure is distorted badly.

Please help me out. What settings do I need to change in order to avoid
such distortion? Is there a possibility that the cnt topology was wrong to
begin with?



The CNT topology is clearly wrong.  It's probably missing some bonds or 
something.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization problem

[Justin Lemkul]

On 6/1/15 9:07 AM, soumadwip ghosh wrote:

Hi Justin,
 the snapshot I uploaded in the URL is of the SSDNA-CNT
system after energy minimization step not before it. I stripped off
water and ions from the system for the ease of visualization. I would
be grateful if you suggest me a possible way out.



I don't see how that changes what I've said.  You have a topology problem with 
the CNT.  Simplify the system - build a smaller CNT, minimize it in vacuo, etc, 
then make it bigger/more complex.  Look at the atoms that are distorting and 
check the existence of their bonded interactions and associated parameters.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization problem

[Justin Lemkul]

On 6/1/15 2:28 AM, soumadwip ghosh wrote:

Hi,
I am simulating a 5X5 carbon nanotube in the presence of nucleic acids
in Tip3P water. I have made this nanotube using VMD nanotube builder and
made the topology using pdb2gmx. Upto the energy minimization step every
thing was fine but when I proceed for energy minimization I get the carbon
naotube crumpled when I view the em.gro file in VMD. It is worth mentioning


Please upload an image somewhere and provide the URL.


that the nucleic acid remains unchanged during the em process and when I am
going for NVT equilibration it does not produce any LINCS warning or stuffs
like that. So is it happening because a visualization tool is unaware of
the molecular topology or do I need to change some parameters in the em.mdp
file?



Possibly; see below.


The cnt.itp file is as follows (partwise)



Incomplete topologies are not generally useful.


;   File 'cnt.top' was generated
;   By user: onbekend (0)
;   On host: onbekend
;   At date: Sat May 30 11:07:23 2015
;
;   This is a standalone topology file
;
;   It was generated using program:
;   pdb2gmx_d - VERSION 4.5.6
;
;   Command line was:
;   pdb2gmx_d -f nishCNT.pdb -o init.gro -p cnt.top
;
;   Force field was read from current directory or a relative path -
path addeed


[ moleculetype ]
; Namenrexcl
SDG 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB  massB
; residue   0 SDG rtp SDG  q  0.0
  1 CA  0SDG C1  1  0 12.011   ;
qtot 0
  2 CA  0SDG C2  2  0 12.011   ;
qtot 0
  3 CA  0SDG C3  3  0 12.011   ;
qtot 0
  4 CA  0SDG C4  4  0 12.011   ;
qtot 0
  5 CA  0SDG C5  5  0 12.011   ;
qtot 0
  6 CA  0SDG C6  6  0 12.011   ;
qtot 0
  7 CA  0SDG C7  7  0 12.011   ;
qtot 0
  8 CA  0SDG C8  8  0 12.011   ;
qtot 0
  9 CA  0SDG C9  9  0 12.011   ;
qtot 0
 10 CA  0SDGC10 10  0 12.011   ;
qtot 0
 11 CA  0SDGC11 11  0 12.011   ;
qtot 0
 12 CA  0SDGC12 12  0 12.011   ;
qtot 0
 13 CA  0SDGC13 13  0 12.011   ;
qtot 0
 14 CA  0SDGC14 14  0 12.011   ;
qtot 0
 15 CA  0SDGC15 15  0 12.011   ;
qtot 0
 16 CA  0SDGC16 16  0 12.011   ;
qtot 0
 17 CA  0SDGC17 17  0 12.011   ;
qtot 0

[ bonds ]
;  aiaj funct   b0 kb
 1 2 1C6   H30.108  284512.0
 1 6 1C5   H40.108  284512.0
 1   403 1   0.108  284512.0
 2 3 1C4   C70.1375 255224.0
 2   385 1C370 C386  0.1375 255224.0
 3 4 1C5  C100.1375 255224.0
 3 7 1C8 C3690.1375 255224.0
 4 5 1C6 C4000.1375 255224.0
 5   400 1C383 C399  0.1375 255224.0
 6   404 1   0.108  284512.0
 7 8 1C9  C110.1375 255224.0
 8 9 1C10  C14   0.1375 255224.0
 811 1C12 C353   0.1375 255224.0
 910 1C4 C3840.1375 255224.0
 914 1C13 C368   0.1375 255224.0
1112 1C13  C15   0.1375 255224.0
11   353 1C338 C354  0.1375 255224.0
1213 1C14  C18   0.1375 255224.0
1215 1C16 C337   0.1375 255224.0
1318 1C17 C352   0.1375 255224.0
14   368 1C351 C367  0.1375 255224.0
1516 1C17  C19   0.1375 255224.0
15   337 1C322 C338  0.1375 255224.0
[ angles ]
;  aiajak functth0   cthubo
cub
 2 1 6 5   120.00334.72 0.24162
29288.0
 2 1   403 5   120.00251.04 0.21525
18409.6
 6 1   403 5   120.00251.04 0.21525
18409.6
 1 2 3 5   120.00334.72 0.24162
29288.0
 1 2   385 5   120.00334.72 0.24162
29288.0
 3 2   385 5   120.00334.72 0.24162
29288.0
 2 3 4 5   

Re: [gmx-users] energy minimization problem

[soumadwip ghosh]

Hi Justin,
the snapshot I uploaded in the URL is of the SSDNA-CNT
system after energy minimization step not before it. I stripped off
water and ions from the system for the ease of visualization. I would
be grateful if you suggest me a possible way out.

Regards,
Soumadwip
Research Fellow
IITB
India
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Re: [gmx-users] energy minimization problem

[soumadwip ghosh]

Thanks Justin for your quick reply. What are the correct non-bonding
settings for CHARMM to be used in the .mdp file?

Here is how the CNT molecule looks like prior to energy minimization.

pre energy min CNT
https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing

I am not continuing any of the equilibration steps anymore. As you can see
the CNT structure is distorted badly.

Please help me out. What settings do I need to change in order to avoid
such distortion? Is there a possibility that the cnt topology was wrong to
begin with?

Regards,
Soumadwip
Research Fellow
IITB
India
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Re: [gmx-users] energy minimization problem

[Ming Tang]

Hi Tsjerk,

I just tried, but it stopped for too many LICS warnings at step 6000. Small 
triple helix can be equilibrated for 1000ns with NPT.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

Can you run in NVT? Then afterwards you can try NPT without position restraints.

Cheers,

Tsjerk
On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

 Thanks a lot, Justin

 It really makes me feel weird. The small triple helix with 30 amino 
 acids per chain(generated simply by deleting other atoms in .pdb file 
 of the real triple helix) can be equilibrated for 1ns using exactly 
 the same control files, and the real triple helix can be used for full 
 atomic simulation without any problem. The CG topology is generated 
 using the same mitinize.py downloaded from the website. I will try for 
 another time, and will tell you if I fix it.

 Thanks.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
 Lemkul
 Sent: Sunday, 17 May 2015 7:07 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] energy minimization problem



 On 5/16/15 8:30 AM, Ming Tang wrote:
  Dear Justin,
 
  I tried to use small time step. First,  set dt=0.005ps, after 
  running
 20ps, I found one chain of the triple helix just went to another water 
 box totally. I guess there is something wrong with the martini ff 
 because of the small time step.
  Then, I increased it to 0.01ps, after running 40ps, I checked the 
  .gro,
 and found all the three chains stay together, which is reasonable. 
 However, even use dt=0.01, the simulation can only run about 1ns. And, 
 after simulating 100 ps using dt=0.01ps, the simulation can just run 
 thousands of steps when dt is increased to 0.02ps. I tried many times 
 and many different time steps, but still could not see the possibility 
 for it to run hundreds of  nanoseconds, which is quite normal when 
 using martini force. If the system can be further minimized, then it can run 
 longer maybe.
 

 This seems entirely random and suggests instead that there is 
 something simply physically unstable with the system or problematic in the 
 topology.
 I don't use MARTINI (or CG models in general) so there's little else I 
 can suggest.  Maybe someone more experienced with such systems will chime in.

 Also note that a chain moving into another box is probably just a 
 PBC effect and not a true dissociation.  If it is a dissociation, it's 
 not simply because of the time step.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441 
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
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Re: [gmx-users] energy minimization problem

[Ming Tang]

Thanks a lot, Justin

It really makes me feel weird. The small triple helix with 30 amino acids per 
chain(generated simply by deleting other atoms in .pdb file of the real triple 
helix) can be equilibrated for 1ns using exactly the same control files, and 
the real triple helix can be used for full atomic simulation without any 
problem. The CG topology is generated using the same mitinize.py downloaded 
from the website. I will try for another time, and will tell you if I fix it.

Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Sunday, 17 May 2015 7:07 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem



On 5/16/15 8:30 AM, Ming Tang wrote:
 Dear Justin,

 I tried to use small time step. First,  set dt=0.005ps, after running 20ps, I 
 found one chain of the triple helix just went to another water box totally. I 
 guess there is something wrong with the martini ff because of the small time 
 step.
 Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and 
 found all the three chains stay together, which is reasonable. However, even 
 use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 
 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is 
 increased to 0.02ps. I tried many times and many different time steps, but 
 still could not see the possibility for it to run hundreds of  nanoseconds, 
 which is quite normal when using martini force. If the system can be further 
 minimized, then it can run longer maybe.


This seems entirely random and suggests instead that there is something simply 
physically unstable with the system or problematic in the topology.  I don't 
use MARTINI (or CG models in general) so there's little else I can suggest.  
Maybe someone more experienced with such systems will chime in.

Also note that a chain moving into another box is probably just a PBC effect 
and not a true dissociation.  If it is a dissociation, it's not simply because 
of the time step.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization problem

[Tsjerk Wassenaar]

Hi Ming Tang,

Can you run in NVT? Then afterwards you can try NPT without position
restraints.

Cheers,

Tsjerk
On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

 Thanks a lot, Justin

 It really makes me feel weird. The small triple helix with 30 amino acids
 per chain(generated simply by deleting other atoms in .pdb file of the real
 triple helix) can be equilibrated for 1ns using exactly the same control
 files, and the real triple helix can be used for full atomic simulation
 without any problem. The CG topology is generated using the same
 mitinize.py downloaded from the website. I will try for another time, and
 will tell you if I fix it.

 Thanks.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
 Lemkul
 Sent: Sunday, 17 May 2015 7:07 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] energy minimization problem



 On 5/16/15 8:30 AM, Ming Tang wrote:
  Dear Justin,
 
  I tried to use small time step. First,  set dt=0.005ps, after running
 20ps, I found one chain of the triple helix just went to another water box
 totally. I guess there is something wrong with the martini ff because of
 the small time step.
  Then, I increased it to 0.01ps, after running 40ps, I checked the .gro,
 and found all the three chains stay together, which is reasonable. However,
 even use dt=0.01, the simulation can only run about 1ns. And, after
 simulating 100 ps using dt=0.01ps, the simulation can just run thousands of
 steps when dt is increased to 0.02ps. I tried many times and many different
 time steps, but still could not see the possibility for it to run hundreds
 of  nanoseconds, which is quite normal when using martini force. If the
 system can be further minimized, then it can run longer maybe.
 

 This seems entirely random and suggests instead that there is something
 simply physically unstable with the system or problematic in the topology.
 I don't use MARTINI (or CG models in general) so there's little else I can
 suggest.  Maybe someone more experienced with such systems will chime in.

 Also note that a chain moving into another box is probably just a PBC
 effect and not a true dissociation.  If it is a dissociation, it's not
 simply because of the time step.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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 send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] energy minimization problem

[Tsjerk Wassenaar]

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size
of the system. It often helps to equilibrate on a limited number of cores,
but I'm not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you
use the relaxed structure from the atomistic simulation? How did you
solvate the system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino
  acids per chain(generated simply by deleting other atoms in .pdb file
  of the real triple helix) can be equilibrated for 1ns using exactly
  the same control files, and the real triple helix can be used for full
  atomic simulation without any problem. The CG topology is generated
  using the same mitinize.py downloaded from the website. I will try for
  another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
  Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after
   running
  20ps, I found one chain of the triple helix just went to another water
  box totally. I guess there is something wrong with the martini ff
  because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. And,
  after simulating 100 ps using dt=0.01ps, the simulation can just run
  thousands of steps when dt is increased to 0.02ps. I tried many times
  and many different time steps, but still could not see the possibility
  for it to run hundreds of  nanoseconds, which is quite normal when
  using martini force. If the system can be further minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is
  something simply physically unstable with the system or problematic in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else I
  can suggest.  Maybe someone more experienced with such systems will
 chime in.
 
  Also note that a chain moving into another box is probably just a
  PBC effect and not a true dissociation.  If it is a dissociation, it's
  not simply because of the time step.
 
  -Justin
 
  --
  ==
 
  Justin A. Lemkul, Ph.D.
  Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences
  School of Pharmacy
  Health Sciences Facility II, Room 629
  University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalem...@outerbanks.umaryland.edu | (410) 706-7441
  http://mackerell.umaryland.edu/~jalemkul
 
  ==
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
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Re: [gmx-users] energy minimization problem

[Ming Tang]

Hi Tsjerk,

My computer has 8 cores only, martini simulation looks much faster than full 
atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys 
-p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o 
minimization-vaccum.tpr
mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there 
anything wrong?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of 
the system. It often helps to equilibrate on a limited number of cores, but I'm 
not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use 
the relaxed structure from the atomistic simulation? How did you solvate the 
system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position 
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino 
  acids per chain(generated simply by deleting other atoms in .pdb 
  file of the real triple helix) can be equilibrated for 1ns using 
  exactly the same control files, and the real triple helix can be 
  used for full atomic simulation without any problem. The CG topology 
  is generated using the same mitinize.py downloaded from the website. 
  I will try for another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
  Justin Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after 
   running
  20ps, I found one chain of the triple helix just went to another 
  water box totally. I guess there is something wrong with the martini 
  ff because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the 
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. 
  And, after simulating 100 ps using dt=0.01ps, the simulation can 
  just run thousands of steps when dt is increased to 0.02ps. I tried 
  many times and many different time steps, but still could not see 
  the possibility for it to run hundreds of  nanoseconds, which is 
  quite normal when using martini force. If the system can be further 
  minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is 
  something simply physically unstable with the system or problematic 
  in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else 
  I can suggest.  Maybe someone more experienced with such systems 
  will
 chime in.
 
  Also note that a chain moving into another box is probably just a 
  PBC effect and not a true dissociation.  If it is a dissociation, 
  it's not simply because of the time step.
 
  -Justin
 
  --
  ==
 
  Justin A. Lemkul, Ph.D.
  Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences School of Pharmacy Health 
  Sciences Facility II, Room 629 University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalem...@outerbanks.umaryland.edu | (410) 706-7441 
  http://mackerell.umaryland.edu/~jalemkul
 
  ==
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
  posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe

Re: [gmx-users] energy minimization problem

[Ming Tang]

Hi Tsjerk,

I used the original structure generated by sabbac.

My computer has 8 cores only, martini simulation looks much faster than full 
atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys 
-p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o 
minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there 
anything wrong?


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of 
the system. It often helps to equilibrate on a limited number of cores, but I'm 
not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use 
the relaxed structure from the atomistic simulation? How did you solvate the 
system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position 
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino 
  acids per chain(generated simply by deleting other atoms in .pdb 
  file of the real triple helix) can be equilibrated for 1ns using 
  exactly the same control files, and the real triple helix can be 
  used for full atomic simulation without any problem. The CG topology 
  is generated using the same mitinize.py downloaded from the website.
  I will try for another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
  Justin Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after 
   running
  20ps, I found one chain of the triple helix just went to another 
  water box totally. I guess there is something wrong with the martini 
  ff because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the 
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. 
  And, after simulating 100 ps using dt=0.01ps, the simulation can 
  just run thousands of steps when dt is increased to 0.02ps. I tried 
  many times and many different time steps, but still could not see 
  the possibility for it to run hundreds of  nanoseconds, which is 
  quite normal when using martini force. If the system can be further 
  minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is 
  something simply physically unstable with the system or problematic 
  in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else 
  I can suggest.  Maybe someone more experienced with such systems 
  will
 chime in.
 
  Also note that a chain moving into another box is probably just a 
  PBC effect and not a true dissociation.  If it is a dissociation, 
  it's not simply because of the time step.
 
  -Justin
 
  --
  ==
 
  Justin A. Lemkul, Ph.D.
  Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences School of Pharmacy Health 
  Sciences Facility II, Room 629 University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalem...@outerbanks.umaryland.edu | (410) 706-7441 
  http://mackerell.umaryland.edu/~jalemkul
 
  ==
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
  posting!
 
  * Can't post? Read http

Re: [gmx-users] energy minimization problem

[Ming Tang]

Besides, the martini.itp does not contain  moleculetype CL, so I edit it like 
this:

[ moleculetype ]
; molname   nrexcl
  CL1

[ atoms ]
;id typeresnr   residu  atomcgnrcharge
 1  P4  1   CL  CL  1   -1

Please help to have a look. I do not know whether it is true or not, as the 
small triple helix used for test does not carry charge, so I did not add CL.

Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming 
Tang
Sent: Monday, 18 May 2015 7:04 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem




Hi Tsjerk,

I used the original structure generated by sabbac.

My computer has 8 cores only, martini simulation looks much faster than full 
atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys 
-p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o 
minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there 
anything wrong?


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of 
the system. It often helps to equilibrate on a limited number of cores, but I'm 
not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use 
the relaxed structure from the atomistic simulation? How did you solvate the 
system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position 
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino 
  acids per chain(generated simply by deleting other atoms in .pdb 
  file of the real triple helix) can be equilibrated for 1ns using 
  exactly the same control files, and the real triple helix can be 
  used for full atomic simulation without any problem. The CG topology 
  is generated using the same mitinize.py downloaded from the website.
  I will try for another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
  Justin Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after 
   running
  20ps, I found one chain of the triple helix just went to another 
  water box totally. I guess there is something wrong with the martini 
  ff because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the 
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. 
  And, after simulating 100 ps using dt=0.01ps, the simulation can 
  just run thousands of steps when dt is increased to 0.02ps. I tried 
  many times and many different time steps, but still could not see 
  the possibility for it to run hundreds of  nanoseconds, which is 
  quite normal when using martini force. If the system can be further 
  minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is 
  something simply physically unstable with the system or problematic 
  in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else 
  I can suggest.  Maybe someone more experienced with such systems 
  will
 chime in.
 
  Also note that a chain moving into another box is probably just a 
  PBC effect and not a true dissociation.  If it is a dissociation

Re: [gmx-users] energy minimization problem

[Ming Tang]

Hi Tsjerk,

This protein has a total charge of 35e, and I added 35 CL to balance the 
system. Is there any difference between adding CL and not adding CL?
Thank you.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

Can you run in NVT? Then afterwards you can try NPT without position restraints.

Cheers,

Tsjerk
On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

 Thanks a lot, Justin

 It really makes me feel weird. The small triple helix with 30 amino 
 acids per chain(generated simply by deleting other atoms in .pdb file 
 of the real triple helix) can be equilibrated for 1ns using exactly 
 the same control files, and the real triple helix can be used for full 
 atomic simulation without any problem. The CG topology is generated 
 using the same mitinize.py downloaded from the website. I will try for 
 another time, and will tell you if I fix it.

 Thanks.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
 Lemkul
 Sent: Sunday, 17 May 2015 7:07 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] energy minimization problem



 On 5/16/15 8:30 AM, Ming Tang wrote:
  Dear Justin,
 
  I tried to use small time step. First,  set dt=0.005ps, after 
  running
 20ps, I found one chain of the triple helix just went to another water 
 box totally. I guess there is something wrong with the martini ff 
 because of the small time step.
  Then, I increased it to 0.01ps, after running 40ps, I checked the 
  .gro,
 and found all the three chains stay together, which is reasonable. 
 However, even use dt=0.01, the simulation can only run about 1ns. And, 
 after simulating 100 ps using dt=0.01ps, the simulation can just run 
 thousands of steps when dt is increased to 0.02ps. I tried many times 
 and many different time steps, but still could not see the possibility 
 for it to run hundreds of  nanoseconds, which is quite normal when 
 using martini force. If the system can be further minimized, then it can run 
 longer maybe.
 

 This seems entirely random and suggests instead that there is 
 something simply physically unstable with the system or problematic in the 
 topology.
 I don't use MARTINI (or CG models in general) so there's little else I 
 can suggest.  Maybe someone more experienced with such systems will chime in.

 Also note that a chain moving into another box is probably just a 
 PBC effect and not a true dissociation.  If it is a dissociation, it's 
 not simply because of the time step.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441 
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
 posting!

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 
 send a mail to gmx-users-requ...@gromacs.org.
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
 posting!

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 
 send a mail to gmx-users-requ...@gromacs.org.

--
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* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.
-- 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] energy minimization error

[Justin Lemkul]

On 5/16/15 11:35 PM, James Lord wrote:

Hi Justin
Thanks for this. Can you tell me which step(s) this bond length is defined
What should I do (redo) to resolve this issue?


The bonds are defined in the topology.  The DD algorithm reads what's in the 
coordinate file and builds cells based on the geometry it finds there.


Without a full description of what's in your system, what steps you've taken to 
prepare it (full commands, in order), there's little I can suggest because it 
would all be guesswork.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] energy minimization error

[Justin Lemkul]

On 5/16/15 6:27 AM, James Lord wrote:

Dear gmx users,
I am getting this error, Can anyone help me to get around this?
Cheers
James


Program mdrun, VERSION 4.6.3
Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 6.93203 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition



Log file opened on Sat May 16 22:15:44 2015
Host: james-E530  pid: 22300  nodeid: 0  nnodes:  1
Gromacs version:VERSION 4.6.3
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Wed Oct 30 18:28:46 NZDT 2013
Built by:   james@james-E530 [CMAKE]
Build OS/arch:  Linux 3.11.0-12-generic x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz
Build CPU family:   6   Model: 58   Stepping: 9
Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1
C compiler flags:   -mavx-Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter
-Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
-DNDEBUG


  :-)  G  R  O  M  A  C  S  (-:

   Gromacs Runs On Most of All Computer Systems

 :-)  VERSION 4.6.3  (-:

 Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
  Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
 Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

Berk Hess, David van der Spoel, and Erik Lindahl.

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  Copyright (c) 2001-2012,2013, The GROMACS development team at
 Uppsala University  The Royal Institute of Technology, Sweden.
 check out http://www.gromacs.org for more information.

  This program is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
 as published by the Free Software Foundation; either version 2.1
  of the License, or (at your option) any later version.

 :-)  mdrun  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
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  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
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 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
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GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  

Input Parameters:
integrator   = steep
nsteps   = 5
init-step= 0
cutoff-scheme= Group
ns_type  = Grid
nstlist  = 5
ndelta   = 2
nstcomm  = 100
comm-mode= Linear
nstlog   = 1000
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstcalcenergy= 100
nstenergy= 1000
nstxtcout= 0
init-t   = 0
delta-t  = 0.001
xtcprec  = 1000
fourierspacing   = 0.12
nkx  = 56
nky  = 56
nkz  = 144
pme-order= 4
ewald-rtol   = 1e-05
ewald-geometry   = 0
epsilon-surface  

Re: [gmx-users] energy minimization problem

[Justin Lemkul]

On 5/14/15 10:02 PM, Ming Tang wrote:

Hi Justin

Here is the .mdp file with position restraints, which I downloaded from the 
martini tutorial website. It works well with the tutorial and my small triple 
helix, and the grompp process does not give any warnings. Please help to have a 
look. Many thanks to you.

define   =  -DPOSRES
integrator   =  md
dt   =  0.02


Have you tried simply reducing the time step?  20 fs may be reasonable for a 
well equilibrated system, but if the run is dying early, then this is the first 
thing I would look at.


-Justin


nsteps   =  5
nstxout  =  0
nstvout  =  0
nstlog   =  1000
nstxtcout=  1000
xtc-precision=  10
cutoff-scheme=verlet
coulombtype  = reaction-field-zero
coulomb-modifier = potential-shift-verlet
rcoulomb-switch  =  0.9
rcoulomb =  1.4
epsilon_r=  15
vdw-modifier =  force-switch
rvdw-switch  =  0.9
rvdw =  1.4
tcoupl   =  v-rescale
tc-grps  =  Protein W
tau-t=  1.0 1.0
ref-t=  310 310
compressibility  =  3e-4
ref-p=  1.0
refcoord_scaling =  all
pbc  =  xyz

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Friday, 15 May 2015 11:50 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem



On 5/14/15 9:47 PM, Ming Tang wrote:

Dear Justin,

I saw it in the terminal.

Potential Energy  = -6.3682131e+05
Maximum force =  1.8876091e+02 on atom 1147
Norm of force =  3.1155257e+00

But, how can I further minimize my protein?



Minimization is not your problem.  Post a full .mdp file of the run that is 
failing.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization problem

[Justin Lemkul]

On 5/15/15 9:32 AM, Ming Tang wrote:

Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be 
reasonable according to gromacs website. So ijust kept trying 0.02ps



The time step will depend on the stability of the system, which in turn depends 
on how well equilibrated it is.  If reducing the time step promotes stability 
during equilibration, that is the most obvious solution.  After equilibrating 
for a while, try increasing the time step.


-Justin


Sent from my Huawei Mobile

Justin Lemkul jalem...@vt.edu wrote:



On 5/14/15 10:02 PM, Ming Tang wrote:

Hi Justin

Here is the .mdp file with position restraints, which I downloaded from the 
martini tutorial website. It works well with the tutorial and my small triple 
helix, and the grompp process does not give any warnings. Please help to have a 
look. Many thanks to you.

define   =  -DPOSRES
integrator   =  md
dt   =  0.02


Have you tried simply reducing the time step?  20 fs may be reasonable for a
well equilibrated system, but if the run is dying early, then this is the first
thing I would look at.

-Justin


nsteps   =  5
nstxout  =  0
nstvout  =  0
nstlog   =  1000
nstxtcout=  1000
xtc-precision=  10
cutoff-scheme=verlet
coulombtype  = reaction-field-zero
coulomb-modifier = potential-shift-verlet
rcoulomb-switch  =  0.9
rcoulomb =  1.4
epsilon_r=  15
vdw-modifier =  force-switch
rvdw-switch  =  0.9
rvdw =  1.4
tcoupl   =  v-rescale
tc-grps  =  Protein W
tau-t=  1.0 1.0
ref-t=  310 310
compressibility  =  3e-4
ref-p=  1.0
refcoord_scaling =  all
pbc  =  xyz

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Friday, 15 May 2015 11:50 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem



On 5/14/15 9:47 PM, Ming Tang wrote:

Dear Justin,

I saw it in the terminal.

Potential Energy  = -6.3682131e+05
Maximum force =  1.8876091e+02 on atom 1147
Norm of force =  3.1155257e+00

But, how can I further minimize my protein?



Minimization is not your problem.  Post a full .mdp file of the run that is 
failing.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization problem

[Ming Tang]

Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be 
reasonable according to gromacs website. So ijust kept trying 0.02ps

Sent from my Huawei Mobile

Justin Lemkul jalem...@vt.edu wrote:



On 5/14/15 10:02 PM, Ming Tang wrote:
 Hi Justin

 Here is the .mdp file with position restraints, which I downloaded from the 
 martini tutorial website. It works well with the tutorial and my small triple 
 helix, and the grompp process does not give any warnings. Please help to have 
 a look. Many thanks to you.

 define   =  -DPOSRES
 integrator   =  md
 dt   =  0.02

Have you tried simply reducing the time step?  20 fs may be reasonable for a
well equilibrated system, but if the run is dying early, then this is the first
thing I would look at.

-Justin

 nsteps   =  5
 nstxout  =  0
 nstvout  =  0
 nstlog   =  1000
 nstxtcout=  1000
 xtc-precision=  10
 cutoff-scheme=verlet
 coulombtype  = reaction-field-zero
 coulomb-modifier = potential-shift-verlet
 rcoulomb-switch  =  0.9
 rcoulomb =  1.4
 epsilon_r=  15
 vdw-modifier =  force-switch
 rvdw-switch  =  0.9
 rvdw =  1.4
 tcoupl   =  v-rescale
 tc-grps  =  Protein W
 tau-t=  1.0 1.0
 ref-t=  310 310
 compressibility  =  3e-4
 ref-p=  1.0
 refcoord_scaling =  all
 pbc  =  xyz

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
 Justin Lemkul
 Sent: Friday, 15 May 2015 11:50 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] energy minimization problem



 On 5/14/15 9:47 PM, Ming Tang wrote:
 Dear Justin,

 I saw it in the terminal.

 Potential Energy  = -6.3682131e+05
 Maximum force =  1.8876091e+02 on atom 1147
 Norm of force =  3.1155257e+00

 But, how can I further minimize my protein?


 Minimization is not your problem.  Post a full .mdp file of the run that is 
 failing.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441 
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at 
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
 mail to gmx-users-requ...@gromacs.org.


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization problem

[Ming Tang]

Dear Justin,

could you please tell me how to get the maximum force of an exact atom? I tried 
g_traj -of, but did not get any force data.
Thanks a lot.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Friday, 15 May 2015 2:40 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem



On 5/14/15 3:12 AM, Ming Tang wrote:
 Dear all,

 I am working with a triple helix containing around 1000 amino acids per chain 
 using martini force field. After energy minimization until it cannot be 
 minimized any more, I moved to NPT, but got LINCS error after thousands of 
 steps. Following Justin's advice on LINCS error, I checked all of the 
 possible causes in blowing up page, but still did not find the reason. Later, 
 I created a smaller model including 30 amino acids per chain, and found it 
 could be move forward to dynamic simulation smoothly using the same control 
 files. Does this mean that my control files are ok?
 I noticed that the minimization was not good enough when working with my real 
 triple helix, as it got stuck in a certain atom (Epot does not change). I 
 have tried to change to use cg algorithm, but got no improvement. Could 
 anybody tell me how to further minimize my triple helix. I got stuck here for 
 3 days.


Sounds like your initial geometry is just bad.  Inspect the surroundings of the 
atom with maximum force; that usually gives an indication of what's going on.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization problem

[Justin Lemkul]

On 5/14/15 9:47 PM, Ming Tang wrote:

Dear Justin,

I saw it in the terminal.

Potential Energy  = -6.3682131e+05
Maximum force =  1.8876091e+02 on atom 1147
Norm of force =  3.1155257e+00

But, how can I further minimize my protein?



Minimization is not your problem.  Post a full .mdp file of the run that is 
failing.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] Energy minimization error for electroporation simulation of DPPC membrane

[Justin Lemkul]

On 4/28/15 8:14 AM, Abhijit Jassem wrote:

Hi all,

I am a beginner to GROMACS and MD simulations in general. I’m trying to
model electroporation in a DPPC membrane but I am having issues with the
energy minimization step. I am basing my approach on the one followed in
Dr. Justin Lemkul’s KALP-15 in DPPC Tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)
but without the steps that use the KALP peptide. After I solvate my
membrane, I am trying to run energy minimization, but my steps are moving
much slower than normal and I get the error Water molecule starting at
atom 109448 can not be settled. Check for bad contacts and/or reduce the


Well, what's going on around atom 109448?


timestep if appropriate.” When I looked this error up, I found that
this suggested that I had a bad starting structure, possibly with atoms
overlapping. Based on this, I assume this error originates when I solvate
my membrane. I am currently using the spc216.gro model. Is this an issue
with my water model or am I doing something else wrong?



There are plenty of potential problems, unfortunately not enough information to 
go on.  Simply using SPC isn't a problem, but something either in the 
configuration or the force field is an issue.  Rather than building a large 
system (you have over 100,000 atoms), do something small, like the pre-built 
DPPC bilayer that the tutorial uses.  That's a sanity check.  If that minimizes 
and equilibrates well, that means the force field is fine and something is wrong 
with the way you built your larger system.  If you want help with that, you have 
to tell us exactly what you're doing (exact command sequence).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization for Inositol pyrophosphate

[Justin Lemkul]

On 2/25/15 1:15 AM, ashish bihani wrote:

Hello, I have understood my mistakes that I reported in previous queries of
this string. now, I am proceeding more systematically.

I have generated ff parameters for Inositol Pyrophosphate with the help of
PRODRG server (as mentioned in the tutorials) as a residue and added it to


Hopefully you're not actually using raw PRODRG parameters, they're generally 
quite inadequate.



aminoacids.rtp. I was able to reformat atoms, bonds, bond angles, dihedrals
and impropers by imitating the format of the definitions of other residues.
But I am not able to find a format for [ pairs ] which I believe is important
for my experiment. Particular pairs defined in ffnonbonded.itp file of
gromos54A7 do not have codes unlike dihedrals. If I have two columns for
individual atoms (e.g. O35 tab P15 tab ?) involved in the interaction, how do
I point the program to corresponding c6 and c12 values in ffnonbonded.itp?



The GROMOS force fields only use special pair interactions for certain 
combinations.  If you haven't parametrized these interactions, it's hard to say 
whether or not you actually need them.  Perhaps you should be looking into a 
more well established force field rather than trying to create one from scratch 
from a questionable web server.



Secondly, the parameter file generated by PRODRG does not contain all the
possible dihedral in Inositokl Pyrophosphate. Are those interactions ignored
because of some criteria or should I add them manually?



You'll have to be more specific about what's missing and why you think it should 
be there.  In general, dihedrals aren't compulsory for every possible bond, but 
the details vary from force field to force field.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization for Inositol pyrophosphate

[ashish bihani]

Hello, 
I have understood my mistakes that I reported in previous queries of this 
string. now, I am proceeding more systematically.

I have generated ff parameters for Inositol Pyrophosphate with the help of 
PRODRG server (as mentioned in the tutorials) as a residue and added it to 
aminoacids.rtp. I was able to reformat atoms, bonds, bond angles, dihedrals and 
impropers by imitating the format of the definitions of other residues. But I 
am not able to find a format for [ pairs ] which I believe is important for my 
experiment. 
Particular pairs defined in ffnonbonded.itp file of gromos54A7 do not have 
codes unlike dihedrals. If I have two columns for individual atoms (e.g. O35 
tab P15 tab ?) involved in the interaction, how do I point the program to 
corresponding c6 and c12 values in ffnonbonded.itp?

Secondly, the parameter file generated by PRODRG does not contain all the 
possible dihedral in Inositokl Pyrophosphate. Are those interactions ignored 
because of some criteria or should I add them manually?

From: ashish.bih...@outlook.com
To: gmx-us...@gromacs.org
Subject: RE: Energy minimization for Inositol pyrophosphate
Date: Fri, 30 Jan 2015 12:25:43 +0530




Hello,

I understand that .itp is a topology file. But the swissparam pack does not 
have a .gro file. How do I create solvated.gro ? (which has to be used in 
grompp) 
Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say 
whether .itp can sustitute the other two.

From: ashish.bih...@outlook.com
To: gmx-us...@gromacs.org
Subject: Energy minimization for Inositol pyrophosphate
Date: Thu, 29 Jan 2015 16:53:56 +0530










Hello all,
I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the 
structure from scratch. I have converted PDB to mol2 with openbabel and 
submitted at Swissparam (http://swissparam.ch/) which returned a zip file 
containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, 
.mol2). 1. Which of these files can be used as force field to generate a 
topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water 
spc
2. The regular ffs among the options do not recognize IP7 as its atoms can not 
be associated with protein/DNA/RNA. All the ffs are based on amino acid 
residues and nucleotides. Is there an atom based ff available for GROMACS which 
I can place in ff directory and include in ff list ? (like MMFF)Swissparam help 
page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 
terminology for those atoms. I am having a hard time figuring out what names 
these atoms should be assigned since all the atoms are unknown. 
I am attaching the pack returned by swissparam and the version of pdb file with 
some name modifications.Thank you.



  
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Re: [gmx-users] Energy minimization for Inositol pyrophosphate

[Justin Lemkul]

On 1/30/15 1:55 AM, ashish bihani wrote:

Hello,

I understand that .itp is a topology file. But the swissparam pack does not 
have a .gro file. How do I create solvated.gro ? (which has to be used in 
grompp)
Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say 
whether .itp can sustitute the other two.



Quoting your original message:

I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the 
structure from scratch


So you have a coordinate file (.gro format is not mandatory).  What's the 
problem?

-Justin


From: ashish.bih...@outlook.com
To: gmx-us...@gromacs.org
Subject: Energy minimization for Inositol pyrophosphate
Date: Thu, 29 Jan 2015 16:53:56 +0530










Hello all,
I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the 
structure from scratch. I have converted PDB to mol2 with openbabel and 
submitted at Swissparam (http://swissparam.ch/) which returned a zip file 
containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, 
.mol2). 1. Which of these files can be used as force field to generate a 
topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water 
spc
2. The regular ffs among the options do not recognize IP7 as its atoms can not 
be associated with protein/DNA/RNA. All the ffs are based on amino acid 
residues and nucleotides. Is there an atom based ff available for GROMACS which 
I can place in ff directory and include in ff list ? (like MMFF)Swissparam help 
page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 
terminology for those atoms. I am having a hard time figuring out what names 
these atoms should be assigned since all the atoms are unknown.
I am attaching the pack returned by swissparam and the version of pdb file with 
some name modifications.Thank you.






--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization for Inositol pyrophosphate

[Justin Lemkul]

On 1/29/15 6:23 AM, ashish bihani wrote:







Hello all,
I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the 
structure from scratch. I have converted PDB to mol2 with openbabel and 
submitted at Swissparam (http://swissparam.ch/) which returned a zip file 
containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, 
.mol2). 1. Which of these files can be used as force field to generate a 
topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water 
spc
2. The regular ffs among the options do not recognize IP7 as its atoms can not 
be associated with protein/DNA/RNA. All the ffs are based on amino acid 
residues and nucleotides. Is there an atom based ff available for GROMACS which 
I can place in ff directory and include in ff list ? (like MMFF)Swissparam help 
page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 
terminology for those atoms. I am having a hard time figuring out what names 
these atoms should be assigned since all the atoms are unknown.
I am attaching the pack returned by swissparam and the version of pdb file with 
some name modifications.Thank you.



If you have an .itp file, that's a topology.  You don't need to run through 
pdb2gmx again, because the purpose of pdb2gmx is to create a topology.  If file 
formats are unfamiliar to you, refer to Chapter 5 of the manual where all of 
this is covered.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization for Inositol pyrophosphate

[ashish bihani]

Hello,

I understand that .itp is a topology file. But the swissparam pack does not 
have a .gro file. How do I create solvated.gro ? (which has to be used in 
grompp) 
Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say 
whether .itp can sustitute the other two.

From: ashish.bih...@outlook.com
To: gmx-us...@gromacs.org
Subject: Energy minimization for Inositol pyrophosphate
Date: Thu, 29 Jan 2015 16:53:56 +0530










Hello all,
I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the 
structure from scratch. I have converted PDB to mol2 with openbabel and 
submitted at Swissparam (http://swissparam.ch/) which returned a zip file 
containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, 
.mol2). 1. Which of these files can be used as force field to generate a 
topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water 
spc
2. The regular ffs among the options do not recognize IP7 as its atoms can not 
be associated with protein/DNA/RNA. All the ffs are based on amino acid 
residues and nucleotides. Is there an atom based ff available for GROMACS which 
I can place in ff directory and include in ff list ? (like MMFF)Swissparam help 
page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 
terminology for those atoms. I am having a hard time figuring out what names 
these atoms should be assigned since all the atoms are unknown. 
I am attaching the pack returned by swissparam and the version of pdb file with 
some name modifications.Thank you.



  
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Gromacs Users mailing list

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Re: [gmx-users] Energy minimization problem in Choline Chloride+Urea mixture in Gromacs

[Justin Lemkul]

On 1/2/15 11:21 AM, Suman Das wrote:

Hi,
  I am trying to simulate a mixture of Choline Chloride+Urea mixture with
33:67 ratio at 298 K. I have taken the force field of choline from this
paper :http://pubs.acs.org/doi/full/10.1021/jp404619x
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp404619x,
chloride from http://pubs.acs.org/doi/full/10.1021/jp063901o
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp063901o
and urea from http://pubs.acs.org/doi/full/10.1021/jp030534x
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp030534x.
During the minimization process Fmax  200 but potential energy was quite
high~5.4465270e+04. And finally the simulation crushes.  I have used this
force field of urea previously which matches well with experimental data.
So I have tried with another force field of choline (
http://pubs.acs.org/doi/full/10.1021/jp301270y
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp301270y)
but exactly the same thing happens. I have also tried the freeze group
option. But the result is same. I built the box using packmol. I took the
initial box length 5nm.



http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization problem in Choline Chloride+Urea mixture in Gromacs

[Christopher Neale]

Can you simulate a single molecule of choline in vacuum without it crashing? 
What about urea?


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Suman Das 
sumandas...@gmail.com
Sent: 02 January 2015 11:21
To: gmx-us...@gromacs.org
Subject: [gmx-users] Energy minimization problem in Choline Chloride+Urea   
mixture in Gromacs

Hi,
 I am trying to simulate a mixture of Choline Chloride+Urea mixture with
33:67 ratio at 298 K. I have taken the force field of choline from this
paper :http://pubs.acs.org/doi/full/10.1021/jp404619x
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp404619x,
chloride from http://pubs.acs.org/doi/full/10.1021/jp063901o
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp063901o
and urea from http://pubs.acs.org/doi/full/10.1021/jp030534x
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp030534x.
During the minimization process Fmax  200 but potential energy was quite
high~5.4465270e+04. And finally the simulation crushes.  I have used this
force field of urea previously which matches well with experimental data.
So I have tried with another force field of choline (
http://pubs.acs.org/doi/full/10.1021/jp301270y
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp301270y)
but exactly the same thing happens. I have also tried the freeze group
option. But the result is same. I built the box using packmol. I took the
initial box length 5nm.

regards,
Suman
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Re: [gmx-users] energy minimization

[Onur TUNA]

Dear md,

I think I understand what you want to say. If you want the energy needed to 
pull away from the binding site, try using Umbrella Sampling method. You will 
get Potential of Mean Force which you are able to calculate binding constant 
directly.

Best
Onur

On 11/14/14 08:52 AM, rama david  ramadavidgr...@gmail.com wrote:
 
 Dear md,
  On docking the only change in enegy for ligand takes place. The protein is
 rigid generally.
 So what was your condition was it regid or flexible for some residues??
 so how it can have the energy the energy of single peptide,single
 protein and the energy of
 docking complex is compared. The docking complex is not always has so much
 less energy.
 which software u used? read the manual of software that may tell about
 there way to compare the enrgy
 and algorithm. what is your aim. what u want to say by analysis??
  Please mention all these then only someone can suggest you any opinion.
 
 With regards,
 Rama david
 
 
 
 
 On Fri, Nov 14, 2014 at 12:06 AM, Justin Lemkul jalem...@vt.edu wrote:
 
 
 
  On 11/13/14 2:14 AM, md kashif wrote:
 
  Dear all
  Can anyone suggest that how to compare change in energy of my protein
  before docking and after docking by a ligand.
  Please suggest any suitable tutorial or paper if possible.
 
 
  You can easily calculate an energy value for the protein (single point
  energy calculation), but it's not a free energy and it's totally force
  field-dependent. Proteins are generally (mostly) rigid during docking, so
  any change in the energy is probably small.
 
  If this is related to your previous posts about the energy value after
  minimization, it's really not a useful quantity because the systems are
  simply different.
 
  -Justin
 
  --
  ==
 
  Justin A. Lemkul, Ph.D.
  Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences
  School of Pharmacy
  Health Sciences Facility II, Room 629
  University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalem...@outerbanks.umaryland.edu | (410) 706-7441
  http://mackerell.umaryland.edu/~jalemkul
 
  ==
 
  --
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 mail to gmx-users-requ...@gromacs.org.
 
 
 
 
 Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu 
 e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde 
 kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta 
 mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez.
 
 
 The information contained in this communication may contain confidential or 
 legally privileged information. Hacettepe University doesn't accept any legal 
 responsibility for the contents and attachments of this message. The sender 
 does not accept any liability for any errors or omissions or any viruses in 
 the context of this message which arise as a result of internet transmission.
 





Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu 
e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde 
kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin 
icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez.

The information contained in this communication may contain confidential or 
legally privileged information. Hacettepe University doesn't accept any legal 
responsibility for the contents and attachments of this message. The sender 
does not accept any liability for any errors or omissions or any viruses in the 
context of this message which arise as a result of internet transmission.


Bu e-posta mesaji kisiye özel olup, gizli bilgiler iceriyor olabilir. Eger bu 
e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde 
kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin 
icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez.


The information contained in this communication may contain confidential or 
legally privileged information. Hacettepe University doesn't accept any legal 
responsibility for the contents and attachments of this message. The sender 
does not accept any liability for any errors or omissions or any viruses in the 
context of this message which 

Re: [gmx-users] energy minimization

[Justin Lemkul]

On 11/13/14 2:14 AM, md kashif wrote:

Dear all
Can anyone suggest that how to compare change in energy of my protein
before docking and after docking by a ligand.
Please suggest any suitable tutorial or paper if possible.



You can easily calculate an energy value for the protein (single point energy 
calculation), but it's not a free energy and it's totally force field-dependent. 
 Proteins are generally (mostly) rigid during docking, so any change in the 
energy is probably small.


If this is related to your previous posts about the energy value after 
minimization, it's really not a useful quantity because the systems are simply 
different.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization

[rama david]

Dear md,
 On docking the only change in enegy for ligand takes place. The protein is
rigid generally.
So what was your condition was it regid or flexible for some residues??
so how it can have the energy  the energy of single peptide,single
protein  and the energy of
docking complex is compared. The docking complex is not always has so much
less energy.
which software u used? read the manual of software that may tell about
there way to compare the enrgy
and algorithm. what is your aim. what u want to say by analysis??
   Please mention all these then only someone can suggest you any opinion.

With regards,
Rama david




On Fri, Nov 14, 2014 at 12:06 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/13/14 2:14 AM, md kashif wrote:

 Dear all
 Can anyone suggest that how to compare change in energy of my protein
 before docking and after docking by a ligand.
 Please suggest any suitable tutorial or paper if possible.


 You can easily calculate an energy value for the protein (single point
 energy calculation), but it's not a free energy and it's totally force
 field-dependent.  Proteins are generally (mostly) rigid during docking, so
 any change in the energy is probably small.

 If this is related to your previous posts about the energy value after
 minimization, it's really not a useful quantity because the systems are
 simply different.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==

 --
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 * Please search the archive at http://www.gromacs.org/
 Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] energy minimization of protein taken from PDB

[Mark Abraham]

Hi,

That value may indicate that the ligand is not horribly out of place,
because the total energy is negative. Showing a favourable binding
interaction is a different matter, for which this is just the tiniest first
step.

Mark

On Tue, Nov 11, 2014 at 9:04 AM, md kashif kashifzamir180...@gmail.com
wrote:

 Dear Dr. Justin Lemkul
 Thanks for your kind suggestion,  I have energy minimized my protein taken
 from PDB. It gives result as  -1.5248922e+06. Taking the energy minimized
 protein generated in .gro file file and docking it with ligand and doining
 energy minimization again, it gives result  as  -1.0504211e+06.
 Is this value correct? Is my ligand showing interaction and bound to my
 protein.  Please help.


 Thanking You
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Re: [gmx-users] energy minimization of protein taken from PDB

[Justin Lemkul]

On 11/10/14 2:36 AM, md kashif wrote:

Dear all
I have downloaded a protein from RCSB, having two chains. In order to go
for energy minimization should I delete one chain as both are similar and
other molecules like SO4, water etc? Is the protein having chain A only can
be used for energy minimization  using tutorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/index.html
I have gromacs 4.6.5 installed on my  i7 processor laptop.



Whether or not you remove the second chain depends on whether or not it has any 
functional significance or if it simply crystallizes as a dimer.  For that, you 
need to read the paper associated with the structure and make your decision.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Energy minimization of an UNKNOWN molecule.

[Justin Lemkul]

On 11/3/14 12:57 AM, Kalyanashis Jana wrote:

Thank you very much... But I am not going to use any parent molecules like
protein or DNA. I would like to perform the gromacs simulation for this
unknown molecule.
First few lines of my topology file..

;
; File 'topol.top' was generated
; By user: kollan (506)
; On host: master.localdomain
; At date: Sun Nov  2 20:28:10 2014
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.6.3
;
; Command line was:
; pdb2gmx -f A-T.pdb -o A-T1.pdb -p topol.top
;
; Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
# include A-T.itp

; 
; Built itp for A-T.mol2
;by user vzoete Mon Oct 27 06:32:46 CET 2014
; 
;

[ atomtypes ] 

  The yellow colored lines are first seven line A-T.itp file And the error
was
Fatal error:
Syntax error - File A-T.itp, line 7
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes

Please help me..



You'll need to show us what is in A-T.itp, because that's where the problem is. 
 Probably you're missing a [defaults] directive, but that's just a guess.


-Justin


On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul jalem...@vt.edu wrote:




On 11/2/14 11:32 AM, Kalyanashis Jana wrote:


Thank you so much... I have tried to run the grompp step according to you.
But it is showing
Fatal error:
Syntax error - File A-T.itp, line 7
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
I have attached the .itp file and .top file.
Please kindly tell me, what to do now..



Force-field level directives must be declared before molecule-level
directives.  So if your ligand requires new bonded or nonbonded parameters,
or new atom types, it must be #included before the declaration of any
[moleculetype].  So put your #include statement for the ligand topology
immediately after the #include statement for the parent force field.

-Justin


  On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia 

rosas.vic...@gmail.com
wrote:

  just put the itp file in your working directory, and include it in the

top file of your system, so that Gromacs can find it.

Hope this helps.

Victor

2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com:


Dear all,
I am trying to run a gromacs simulation using an .itp file of an unknown
molecule ( non protein and DNA). I don't want to put the .itp file in a
forcefield folder and I would like put it in my working directory. Can


you


please tell me, what is procedure to finish the energy minimization?


Please


help me..
Thanks in advance,
Kalyanashis

--
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email: kalyan.chem...@gmail.com
--
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==

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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization of an UNKNOWN molecule.

[Victor Rosas Garcia]

just put the itp file in your working directory, and include it in the
top file of your system, so that Gromacs can find it.

Hope this helps.

Victor

2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com:
 Dear all,
 I am trying to run a gromacs simulation using an .itp file of an unknown
 molecule ( non protein and DNA). I don't want to put the .itp file in a
 forcefield folder and I would like put it in my working directory. Can you
 please tell me, what is procedure to finish the energy minimization? Please
 help me..
 Thanks in advance,
 Kalyanashis

 --
 Kalyanashis Jana
 email: kalyan.chem...@gmail.com
 --
 Gromacs Users mailing list

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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Energy minimization of an UNKNOWN molecule.

[Kalyanashis Jana]

Thank you so much... I have tried to run the grompp step according to you.
But it is showing
Fatal error:
Syntax error - File A-T.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
I have attached the .itp file and .top file.
Please kindly tell me, what to do now..

On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com
wrote:

 just put the itp file in your working directory, and include it in the
 top file of your system, so that Gromacs can find it.

 Hope this helps.

 Victor

 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com:
  Dear all,
  I am trying to run a gromacs simulation using an .itp file of an unknown
  molecule ( non protein and DNA). I don't want to put the .itp file in a
  forcefield folder and I would like put it in my working directory. Can
 you
  please tell me, what is procedure to finish the energy minimization?
 Please
  help me..
  Thanks in advance,
  Kalyanashis
 
  --
  Kalyanashis Jana
  email: kalyan.chem...@gmail.com
  --
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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!
 
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-- 
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email: kalyan.chem...@gmail.com
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Re: [gmx-users] Energy minimization of an UNKNOWN molecule.

[Justin Lemkul]

On 11/2/14 11:32 AM, Kalyanashis Jana wrote:

Thank you so much... I have tried to run the grompp step according to you.
But it is showing
Fatal error:
Syntax error - File A-T.itp, line 7
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
I have attached the .itp file and .top file.
Please kindly tell me, what to do now..



Force-field level directives must be declared before molecule-level directives. 
 So if your ligand requires new bonded or nonbonded parameters, or new atom 
types, it must be #included before the declaration of any [moleculetype].  So 
put your #include statement for the ligand topology immediately after the 
#include statement for the parent force field.


-Justin


On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com
wrote:


just put the itp file in your working directory, and include it in the
top file of your system, so that Gromacs can find it.

Hope this helps.

Victor

2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com:

Dear all,
I am trying to run a gromacs simulation using an .itp file of an unknown
molecule ( non protein and DNA). I don't want to put the .itp file in a
forcefield folder and I would like put it in my working directory. Can

you

please tell me, what is procedure to finish the energy minimization?

Please

help me..
Thanks in advance,
Kalyanashis

--
Kalyanashis Jana
email: kalyan.chem...@gmail.com
--
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* Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization of an UNKNOWN molecule.

[Kalyanashis Jana]

Thank you very much... But I am not going to use any parent molecules like
protein or DNA. I would like to perform the gromacs simulation for this
unknown molecule.
First few lines of my topology file..

;
; File 'topol.top' was generated
; By user: kollan (506)
; On host: master.localdomain
; At date: Sun Nov  2 20:28:10 2014
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.6.3
;
; Command line was:
; pdb2gmx -f A-T.pdb -o A-T1.pdb -p topol.top
;
; Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
# include A-T.itp

; 
; Built itp for A-T.mol2
;by user vzoete Mon Oct 27 06:32:46 CET 2014
; 
;

[ atomtypes ] 

 The yellow colored lines are first seven line A-T.itp file And the error
was
Fatal error:
Syntax error - File A-T.itp, line 7
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes

Please help me..

On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/2/14 11:32 AM, Kalyanashis Jana wrote:

 Thank you so much... I have tried to run the grompp step according to you.
 But it is showing
 Fatal error:
 Syntax error - File A-T.itp, line 7
 Last line read:
 '[ atomtypes ]'
 Invalid order for directive atomtypes
 I have attached the .itp file and .top file.
 Please kindly tell me, what to do now..


 Force-field level directives must be declared before molecule-level
 directives.  So if your ligand requires new bonded or nonbonded parameters,
 or new atom types, it must be #included before the declaration of any
 [moleculetype].  So put your #include statement for the ligand topology
 immediately after the #include statement for the parent force field.

 -Justin


  On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia 
 rosas.vic...@gmail.com
 wrote:

  just put the itp file in your working directory, and include it in the
 top file of your system, so that Gromacs can find it.

 Hope this helps.

 Victor

 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com:

 Dear all,
 I am trying to run a gromacs simulation using an .itp file of an unknown
 molecule ( non protein and DNA). I don't want to put the .itp file in a
 forcefield folder and I would like put it in my working directory. Can

 you

 please tell me, what is procedure to finish the energy minimization?

 Please

 help me..
 Thanks in advance,
 Kalyanashis

 --
 Kalyanashis Jana
 email: kalyan.chem...@gmail.com
 --
 Gromacs Users mailing list

 * Please search the archive at

 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!


 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==

 --
 Gromacs Users mailing list

 * Please search the archive at http://www.gromacs.org/
 Support/Mailing_Lists/GMX-Users_List before posting!

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-- 
Kalyanashis Jana
email: kalyan.chem...@gmail.com
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Re: [gmx-users] Energy minimization problem after editconf step

[neha bharti]

Thanks for your reply Justin

The error is now solve but I don't know this is a right way or not.


The step which I perform previously in which I am facing error:

Packing :

1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat

2) grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr

3) mdrun -v -deffnm em

I did this till 24 iteration then I reached area per lipid 0.70 nm^2



4) Adding Solvent:

a) editconf -f system_shrink.gro -o POPC_box.gro -box 8.68740 8.41864
12.70145

b) genbox -cp  POPC_box.gro -cs spc216.gro -o  POPC_sol.gro



5) Adding Ions

a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr

b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

Select 16 to add 1 possitive ion to sol



6) Energy Minimization

Next, energy minimize the entire system now, using the following commands:

a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr

b) mdrun -v -deffnm em



In energy minimization step
The following error occur

Steepest Descents converged to machine precision in 18 steps,
 but did not reach the requested Fmax  1000.
 Potential Energy  =  6.1499341e+20
 Maximum force =inf on atom 3300
Norm of force =  5.4206209e+1

But if I skip the editconf step 4(a) the the energy minimization is normal.
But i need to increase the box size because my protein is out of the box.


So I did some changes before the packing which gives the correct result.
The steps are as follows:


Before energy minimization of POPC.gro I remove the water (SOL molecule
manually) then increase the box size by

1) editconf -f POPC.gro -o popc_new.gro -box 8.68740 8.41864 15 : With the
help of this command I increase the box size of popc.gro which I have
downloaded. ( Peter C. Lai POPC lipid http://cesium.hyperfine.info/~peter
/gromacs/popc36/ )


2) genbox -cp  POPC_new.gro -cs spc216.gro -o  POPC_new_sol.gro : Add
solvent


3) Energy minimization:
a) grompp -f em.mdp -c POPC_new_sol.gro -p topol_popc.top -o em.tpr
b) mdrun -v -deffnm em

4) trjconv to remove periodicity:

trjconv -s em.tpr -f em.gro -o popc_whole.gro -pbc mol -ur compact

select 0 for system

orient the KALP peptide within this same coordinate frame as popc_whole.gro

editconf -f conf.gro -o conf_newbox.gro -c -box 8.68740 8.41864 12.70145

Rest of the step is same as above after packing I took system_shrink24.gro
without using editconf because I already arrange the size of the box like

 Adding Solvent:

a) genbox -cp  system_shrink24.gro -cs spc216.gro -o  POPC_sol.gro



 Adding Ions

a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr

b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

Select 16 to add 1 possitive ion to sol



6) Energy Minimization

Next, energy minimize the entire system now, using the following commands:

a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr

b) mdrun -v -deffnm em


When I perform by above method my energy minimization occur.
Is this the right way??

Thanks

With Regards

Neha bharty




  Hello All

  I am trying to perform MD for protein ligand complex in popc lipid with
  Charmm36 force field. I follow Justin A. Lemkul tutorial of membrane
  protein simulation.

  I have successfully perform till InflateGRO followed by energy
minimization
  step.

  perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat

grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr

  mdrun -v -deffnm em

  till 24 iteration then I reached area per lipid 0.70 nm^2

  when I visualize the molecule then the box size small in Z axis so in
  editconf step I increase the box size and then add solvent and ion .
when I
  increase the box size with editconf then there is atomic clashes
occur.and
  giving following error:

  Steepest Descents converged to machine precision in 18 steps,
   but did not reach the requested Fmax  1000.
   Potential Energy  =  6.1499341e+20
   Maximum force =inf on atom 3300
 Norm of force =  5.4206209e+1


   When I skip this step (editconf) then the minimization is normal.
 But I need to increase the box size.
 How to increase the box size?


You need to provide the exact commands that you used when manipulating the
box,
otherwise it's pure guesswork.
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Re: [gmx-users] Energy minimization problem after editconf step

[Justin Lemkul]

On 9/2/14, 10:49 AM, neha bharti wrote:

Thanks for your reply Justin

The error is now solve but I don't know this is a right way or not.


The step which I perform previously in which I am facing error:

Packing :

1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat

2) grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr

3) mdrun -v -deffnm em

I did this till 24 iteration then I reached area per lipid 0.70 nm^2



4) Adding Solvent:

a) editconf -f system_shrink.gro -o POPC_box.gro -box 8.68740 8.41864
12.70145

b) genbox -cp  POPC_box.gro -cs spc216.gro -o  POPC_sol.gro



5) Adding Ions

a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr

b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

Select 16 to add 1 possitive ion to sol



6) Energy Minimization

Next, energy minimize the entire system now, using the following commands:

a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr

b) mdrun -v -deffnm em



In energy minimization step
The following error occur

Steepest Descents converged to machine precision in 18 steps,
  but did not reach the requested Fmax  1000.
  Potential Energy  =  6.1499341e+20
  Maximum force =inf on atom 3300
Norm of force =  5.4206209e+1

But if I skip the editconf step 4(a) the the energy minimization is normal.
But i need to increase the box size because my protein is out of the box.


So I did some changes before the packing which gives the correct result.
The steps are as follows:


Before energy minimization of POPC.gro I remove the water (SOL molecule
manually) then increase the box size by

1) editconf -f POPC.gro -o popc_new.gro -box 8.68740 8.41864 15 : With the
help of this command I increase the box size of popc.gro which I have
downloaded. ( Peter C. Lai POPC lipid http://cesium.hyperfine.info/~peter
/gromacs/popc36/ )


2) genbox -cp  POPC_new.gro -cs spc216.gro -o  POPC_new_sol.gro : Add
solvent


3) Energy minimization:
a) grompp -f em.mdp -c POPC_new_sol.gro -p topol_popc.top -o em.tpr
b) mdrun -v -deffnm em

4) trjconv to remove periodicity:

trjconv -s em.tpr -f em.gro -o popc_whole.gro -pbc mol -ur compact

select 0 for system

orient the KALP peptide within this same coordinate frame as popc_whole.gro

editconf -f conf.gro -o conf_newbox.gro -c -box 8.68740 8.41864 12.70145

Rest of the step is same as above after packing I took system_shrink24.gro
without using editconf because I already arrange the size of the box like

  Adding Solvent:

a) genbox -cp  system_shrink24.gro -cs spc216.gro -o  POPC_sol.gro



  Adding Ions

a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr

b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

Select 16 to add 1 possitive ion to sol



6) Energy Minimization

Next, energy minimize the entire system now, using the following commands:

a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr

b) mdrun -v -deffnm em


When I perform by above method my energy minimization occur.
Is this the right way??



If it works, you can't argue with results.  I don't know why the first method 
didn't work, but it appears you've found a solution.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Energy minimization has stopped, but the forces have not converged

[Justin Lemkul]

On 6/25/14, 10:12 AM, Iris Nira Smith wrote:

Hello gromacs users,

I have searched the gmx-users archive and have successfully found multiple 
posts that provide advice on how to troubleshoot my issue. Unfortunately, after 
trying multiple ways to troubleshoot as suggested by each of these posts, I am 
still having the same issue.

I successfully mutated a residue in my .pdb file using VMD mutator and am now 
in the minimization phase using steepest descent step-wise energy minimization. 
The error I keep getting is as follows:

Steepest Descents:
Tolerance (Fmax)   =  1.0e+04
Number of steps= 2000
Step=0, Dmax= 1.0e-02 nm, Epot=  5.18534e+14 Fmax= 3.39138e+04, atom= 3228^M
Step=1, Dmax= 1.0e-02 nm, Epot=  5.18534e+14 Fmax= 1.18748e+04, atom= 
10021^M
Step=2, Dmax= 5.0e-03 nm, Epot=  5.18534e+14 Fmax= 1.73483e+04, atom= 3228^M
Step=3, Dmax= 2.5e-03 nm, Epot=  5.18534e+14 Fmax= 2.44124e+04, atom= 3228^M
Step=4, Dmax= 1.2e-03 nm, Epot=  5.18534e+14 Fmax= 2.88081e+04, atom= 3228^M
Step=5, Dmax= 6.2e-04 nm, Epot=  5.18534e+14 Fmax= 3.12647e+04, atom= 3228^M
Step=6, Dmax= 3.1e-04 nm, Epot=  5.18534e+14 Fmax= 3.25644e+04, atom= 3228^M
Step=7, Dmax= 1.6e-04 nm, Epot=  5.18534e+14 Fmax= 3.32326e+04, atom= 3228^M
Step=8, Dmax= 7.8e-05 nm, Epot=  5.18534e+14 Fmax= 3.35718e+04, atom= 3228^M
Step=9, Dmax= 3.9e-05 nm, Epot=  5.18534e+14 Fmax= 3.37432e+04, atom= 3228^M
Step=   10, Dmax= 2.0e-05 nm, Epot=  5.18534e+14 Fmax= 3.38282e+04, atom= 3228^M
Step=   11, Dmax= 9.8e-06 nm, Epot=  5.18534e+14 Fmax= 3.38707e+04, atom= 3228^M
Step=   12, Dmax= 4.9e-06 nm, Epot=  5.18534e+14 Fmax= 3.38920e+04, atom= 3228^M
Step=   13, Dmax= 2.4e-06 nm, Epot=  5.18534e+14 Fmax= 3.39031e+04, atom= 3228^M
Step=   14, Dmax= 1.2e-06 nm, Epot=  5.18534e+14 Fmax= 3.39092e+04, atom= 3228^M

Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax  1 (whichmay not be possible for your system).
It stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  1.
Potential Energy  =  5.1853375e+14
Maximum force =  3.3913793e+04 on atom 3228
Norm of force =  6.5862207e+02

I have analyzed my .gro file for steric clashes with atom 3228 (HE2 atom on a 
tyrosine located 20 amino acids from c-terminal tail) and the only thing that 
could potentially clash with it is a hydrogen atom on a nearby water which is 
1.2 Angstroms away. I first moved x-coordinate of atom 3228 by 0.1nm (or 1.0 
Angstrom), but the same error occurred. I then removed that entire water 
molecule that was near atom 3228, re-ran the energy minimization and the same 
error occurred. I changed the emtol from 1,000 to 10,000 even to 100,000 and 
the same error occurred. I then analyzed the energy using g_energy, but the 
following error occurred:



Look at the energy terms in the .log file.  Something should stick out like a 
sore thumb here.



---
Program g_energy, VERSION 4.6.3
Source code file: /var/tmp/packages/gromacs-4.6.3/src/gmxlib/enxio.c, line: 828

Fatal error:
Energy file g36r_em2.edr not recognized, maybe different CPU?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I finally started over and created a new configuration (.gro) file as well as a 
topology (.top) file, but the same error occurred. Note: I have 13 other mutant 
model systems that I have run minimization-equilibration successfully but this 
particular mutant model keeps giving me the same repeated error. The potential 
energy of this mutant system as well as the force on atom 3228 is rather high. 
Can you offer any advice or alternate suggestions to troubleshooting this 
error? Should I run a few steps of CG first and then SD?



The fact that the energy is essentially infinite and never changes means it's an 
unresolvable problem.  There is likely something intrinsically wrong with the 
coordinates or the topology.  You're not missing any atoms or causing pdb2gmx to 
do anything strange, are you?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences 

Re: [gmx-users] Energy minimization result problem

[Mark Abraham]

Hi,

Proteins do not have a single holy structure, nor is any given quantity of
MD going to find it, if it exists. Neither is there a single metric of
suitability - backbone strain as measured by Ramachandran plot deviations
could easily be the result of accommodating worse problems while stuck in a
local minimum. You can get zero deviations by unfolding the whole protein,
but that isn't going to tell you anything. Or the deviations could be good
things, because parts of your structure are atypical, but healthy.

Mark
On Apr 13, 2014 9:52 AM, neha_bharty nehabharty...@gmail.com wrote:

 Hello Justin Lemkul

 Thank you very much for your reply.
 I also preformed MD for 15 ns. After MD I check my protein model with
 Ramachandran Plot using Online Procheck server. But the result was same as
 after energy minimization. The residues which were present in allowed
 region
 was again less than that of previous protein.
 As I am new in gromacs I don't have much idea.
 In my view I guess after energy minimization and MD the residues which were
 present in allowed region of Ramachandran plot should be increases.
 And if it decreases it means the previous model is better.
 Is there any other way to check my protein model is better after energy
 minimization and MD or not??

 If require I can also send the .mdb file I have used for MD.



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Re: [gmx-users] Energy minimization result problem

[neha_bharty]

Hello
I am new user of gromacs. I am using gromacs 4.6.3
I wanted to minimize the energy of a protein. Before energy minimization the
prockeck result for Ramachandran plot was 89% in allowed region but after
energy minimization the result become worse i.e. 87%.
I was performing energy minimization to refine the model. But the model
become worse after that.
I Model the protein using homology modeling and needed it for docking

I am also doing it with different protein molecules but again the same
problem occurs.
I don't know that its normal or there is problem with my parameter or force
field.
I am also mentioning the detail of my energy minimization.

The details are: 
Force Field Used: CHARMM27 all-atom force field
Water Model: TIP3P

em.mdp file is:

; VARIOUS PREPROCESSING OPTIONS = 
title= 
cpp  = /lib/cpp
include  = 
define   = -DFLEXIBLE

; RUN CONTROL PARAMETERS = 
integrator   = steep
; start time and timestep in ps = 
tinit= 0
dt   = 0.002
nsteps   = 15000

; ENERGY MINIMIZATION OPTIONS = 
emtol= 10
emstep   = 0.1
nstcgsteep   = 1000

coulombtype =pme
nstenergy   =10

Please help me out for this. 


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Re: [gmx-users] Energy minimization result problem

[Justin Lemkul]

On 4/11/14, 7:47 AM, neha_bharty wrote:

Hello
I am new user of gromacs. I am using gromacs 4.6.3
I wanted to minimize the energy of a protein. Before energy minimization the
prockeck result for Ramachandran plot was 89% in allowed region but after
energy minimization the result become worse i.e. 87%.
I was performing energy minimization to refine the model. But the model
become worse after that.


That's not a huge change, nor is energy minimization rigorous enough to fully 
refine a model.  EM will probably optimize the side chains pretty well, but the 
backbone may require actual MD simulation to sample better conformations.  The 
changes that take place during EM are typically very small.



I Model the protein using homology modeling and needed it for docking

I am also doing it with different protein molecules but again the same
problem occurs.
I don't know that its normal or there is problem with my parameter or force
field.
I am also mentioning the detail of my energy minimization.

The details are:
Force Field Used: CHARMM27 all-atom force field
Water Model: TIP3P



CHARMM36 may be a better option.  The recalibration of the CMAP terms could be 
relevant here.  See http://mackerell.umaryland.edu/CHARMM_ff_params.html to 
download the force field files.


-Justin


em.mdp file is:

; VARIOUS PREPROCESSING OPTIONS =
title=
cpp  = /lib/cpp
include  =
define   = -DFLEXIBLE

; RUN CONTROL PARAMETERS =
integrator   = steep
; start time and timestep in ps =
tinit= 0
dt   = 0.002
nsteps   = 15000

; ENERGY MINIMIZATION OPTIONS =
emtol= 10
emstep   = 0.1
nstcgsteep   = 1000

coulombtype =pme
nstenergy   =10

Please help me out for this.


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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] energy minimization erorr

[Justin Lemkul]

On 11/18/13 2:36 AM, Archana Sonawani-Jagtap wrote:

Hi,

I am simulating a peptide in TFE-water system. I am getting following error:
1 particles communicated to PME node 4 are more than 2/3 times the
cut-off out o f the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.

below is my em.mdp file

integrator  = steep
emtol   = 1000.0
emstep  = 0.01
nsteps  = 5
nstlist = 1
ns_type = grid
rlist   = 1.2
coulombtype = PME
rcoloumb= 1.2
rvdw= 1.2
pbc = xyz

Please help me. Why this error has ocurred and what parameter should I
change to resolve it.


Likely the cutoffs are simply wrong, but you haven't said what the force field 
is.  The other possible sources of problems during EM are (1) bad topology or 
(2) unreasonable starting configuration.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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