[gmx-users] Segmentation fault and PCA Analysis

[Ahmed Mashaly]

Dear users,
I am trying to align my trajectory to an average structure pdb, the problem is 
that I have "Segmentation fault (core dumped)" while taking this pdb as a 
reference structure, while it worked with the em.tpr file ... I also tried to 
extract the pdb from the that em.tpr using gmx editconf and when I used it as a 
reference I faced the same problem, so I guess the peoblem with the pdb format 
... Any suggestions?
Another question about PCA, is there a way to do dot product in GROMACS?
Kind regards,Ahmed
 

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[gmx-users] Rerun

[Ahmed Mashaly]

Dear users,
Will the .trr files produced from rerun of .xtc files be the same if it was 
produced during the original MD simulation?
Kind regards,Ahmed
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[gmx-users] rerun

[Ahmed Mashaly]

Dear users,
Will the .trr file produced from rerun of .xtc files the same if it was 
produced during the original MD simulation?
Kind regards,Ahmed 
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Re: [gmx-users] RMSD values consideration

[Ahmed Mashaly]

Try using trjconv to remove pbc before analysis
Regards,Ahmed 
 
  On Wed, 28 Mar, 2018 at 8:43 am, SHYANTANI MAITI 
wrote:   Dear all,
After using this command for computation of rmsd of backbone of protein
protein complex consisting of three proteins :
/home/locuz/apps/gromacs/5.1/bin/gmx_mpi rms -f md_0_1.trr -s md_0_1.tpr
The rmsd is drastically increasing from 1 to 6 nm and after that it again
decreases to 1nm. can I use this result for my analysis? Is the rmsd
correctly obtained?
-- 
Best regards,
*Shyantani Maiti*
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Re: [gmx-users] rvdw and rcoulomb

[Ahmed Mashaly]

Dear Justin,

What do you mean by incorrect?
I understand it is higher than it should be (0.8 - 1 nm), it will consume more 
time, but won't give wrong results, am I correct? 
Kind Regards,
Ahmed 


From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org 
Sent: Tuesday, March 13, 2018 12:18 PM
Subject: Re: [gmx-users] rvdw and rcoulomb





On 3/13/18 5:17 AM, Ahmed Mashaly wrote:
> Thanks guys
>
> It is AMBER ff
> Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
> for continuation with no effect on the results? And if I do the other 
> restarts starting from 1 or it will give different results?

You shouldn't switch physical models mid-simulation. Start over using 
the correct value (1.2 nm is incorrect for AMBER, anyway).

-Justin

> On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll
>> <pall.szil...@gmail.com> wrote:
>> Note that rcoulomb, unlike rvdw, when using a PME long-range
>> electrostatics, is tunable (together with the PME grid spacing).
>> --
>> Szilárd
>>
>>
>> On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>
>>> On 3/11/18 7:33 PM, Ahmed Mashaly wrote:
>>>> Dear users,
>>>> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind
>>>> Regards,Ahmed
>>>>
>>> These values are a function of the force field and are not freely tunable.
>>>
>>> -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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-- 
==

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] rvdw and rcoulomb

[Ahmed Mashaly]

Thanks guys

It is AMBER ff
Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
for continuation with no effect on the results? And if I do the other restarts 
starting from 1 or it will give different results?

On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll
><pall.szil...@gmail.com> wrote:
>Note that rcoulomb, unlike rvdw, when using a PME long-range
>electrostatics, is tunable (together with the PME grid spacing).
>--
>Szilárd
>
>
>On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>> On 3/11/18 7:33 PM, Ahmed Mashaly wrote:
>>>
>>> Dear users,
>>> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind
>>> Regards,Ahmed
>>>
>> These values are a function of the force field and are not freely tunable.
>>
>> -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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>
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[gmx-users] rvdw and rcoulomb

[Ahmed Mashaly]

Dear users,
Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed

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Re: [gmx-users] NVT NPT restrains

[Ahmed Mashaly]

Hi Justin
I see the point of restraining heavy atoms in NPT.The problem is that; no posre 
are included in the top file generated by Acpype, any suggestion to overcome 
that? Kind Regards,Ahmed



  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Tuesday, February 20, 2018 7:55 PM
 Subject: Re: [gmx-users] NVT NPT restrains
   


On 2/20/18 1:47 PM, Ahmed Mashaly wrote:
> Hi
>
> About the restrains, I see that it is necessary for NVT and NPT.
> For the .top and .gro produced by Acpype,
> https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM
>
> I don't have porse.itp nor anything related to restrain in the .top file, 
> only for water
>
> #ifdef FLEXIBLE
> [ bonds ]
> ; i j  funct  length  force.c.
> 1  2  1  0.09572  462750.4 0.09572  462750.4
> 1  3  1  0.09572  462750.4 0.09572  462750.4
>
>
> So what shall I do in this case? and what is the ideal time for NVT and NPT

Restraints are typically applied to solute heavy atoms to prevent 
distortion from initial, artificial configurations. It is very rare to 
need to restrain water, as that defeats the purpose of equilibration, 
which is primarily to allow the solvent to relax and achieve the desired 
state.

-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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[gmx-users] NVT NPT restrains

[Ahmed Mashaly]

Hi

About the restrains, I see that it is necessary for NVT and NPT.
For the .top and .gro produced by Acpype, 
https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM

I don't have porse.itp nor anything related to restrain in the .top file, only 
for water

#ifdef FLEXIBLE
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572   462750.4 0.09572   462750.4
1   3   1   0.09572   462750.4 0.09572   462750.4


So what shall I do in this case? and what is the ideal time for NVT and NPT
 Kind Regards,
Ahmed
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[gmx-users] Energygrps

[Ahmed Mashaly]

Hi
What is the default engerygrps to be written if I don't specify them in the mdp 
file?
And if I have more than one ligand and want to calculate the energy between 
them and the protein, and also between one part of the protein (loop) and the 
rest of the protein I should make an index identifying each ligand indvidually 
and this part too and my energygrps will be protein lig1 protein lig2 protein 
loop ...
If I don't specify this from the beginning is it the same to get with mdrun 
rerun or will be different? This questions might have been answered before in 
archive, but there is a problem to access it, any idea when will it be resolved?
Kind Regards,Ahmed 

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Re: [gmx-users] simulated annealing

[Ahmed Mashaly]

So I redo the NVT with ref-t and gen-temp set to zero or I neglect this issue? 
Kind Regards,Ahmed 



  From: Justin Lemkul <jalem...@vt.edu>
 To: Discussion list for GROMACS users <gmx-us...@gromacs.org> 
 Sent: Monday, February 19, 2018 8:33 PM
 Subject: Re: [gmx-users] simulated annealing
   


On 2/19/18 2:31 PM, Ahmed Mashaly wrote:
> Thanks, Justin.
>
> I had set it to 300K before (as the original mdp was), but now I found others 
> with 0
>
>
> Now when if we look at the log file, you can see ref temp for both groups 
> starts from 0 and increasing, but the temperature in the details goes from 
> 300 to 5 to 2, then it starts increasing again:
>
> --
> Started mdrun on rank 0 Thu Feb 15 06:00:49 2018
> Step Time
> 0 0.0
>
> Current ref_t for group Protein: 0.0
> Current ref_t for group non-Protein: 0.0
> Energies (kJ/mol)
> Bond Angle Proper Dih. Improper Dih. LJ-14
> 3.51283e+03 1.20582e+04 6.93519e+04 6.27988e+02 1.88294e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.26883e+05 7.62987e+05 -3.36842e+04 -5.35584e+06 1.97969e+04
> Potential Kinetic En. Total Energy Conserved En. Temperature
> -4.27548e+06 7.07199e+05 -3.56828e+06 -3.56828e+06 3.00605e+02
> Pres. DC (bar) Pressure (bar) Constr. rmsd
> -1.86887e+02 1.45163e+03 4.71563e-06
>
> DD step 19 load imb.: force 93.3% pme mesh/force 1.284
>
>
> step 40 Turning on dynamic load balancing, because the performance loss due 
> to load imbalance is 3.6 %.
>
> DD load balancing is limited by minimum cell size in dimension Y
> DD step 499 vol min/aver 0.501! load imb.: force 6.8% pme mesh/force 0.849
>
> Step Time
> 500 1.0
>
> Current ref_t for group Protein: 0.6
> Current ref_t for group non-Protein: 0.6
> Energies (kJ/mol)
> Bond Angle Proper Dih. Improper Dih. LJ-14
> 3.46055e+03 1.23246e+04 6.95866e+04 6.62756e+02 1.87622e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.26321e+05 7.48416e+05 -3.36842e+04 -5.50170e+06 1.60271e+04
> Potential Kinetic En. Total Energy Conserved En. Temperature
> -4.43983e+06 1.20712e+04 -4.42776e+06 -3.56007e+06 5.13104e+00
> Pres. DC (bar) Pressure (bar) Constr. rmsd
> -1.86887e+02 -1.52962e+03 2.60669e-06
>
>
>
> DD load balancing is limited by minimum cell size in dimension Y
> DD step 999 vol min/aver 0.536! load imb.: force 4.4% pme mesh/force 0.719
>
> Step Time
> 1000 2.0
>
> Current ref_t for group Protein: 1.2
> Current ref_t for group non-Protein: 1.2
> Energies (kJ/mol)
> Bond Angle Proper Dih. Improper Dih. LJ-14
> 3.36670e+03 1.22399e+04 6.95391e+04 6.50404e+02 1.87726e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.26254e+05 7.67224e+05 -3.36842e+04 -5.55850e+06 1.52291e+04
> Potential Kinetic En. Total Energy Conserved En. Temperature
> -4.47891e+06 5.32623e+03 -4.47359e+06 -3.56020e+06 2.26399e+00
> Pres. DC (bar) Pressure (bar) Constr. rmsd
> -1.86887e+02 -1.51090e+03 2.52820e-06
>
> DD load balancing is limited by minimum cell size in dimension Y
> DD step 1499 vol min/aver 0.568! load imb.: force 3.1% pme mesh/force 0.727
>
> Step Time
> 1500 3.0
>
> Current ref_t for group Protein: 1.8
> Current ref_t for group non-Protein: 1.8
> Energies (kJ/mol)
> Bond Angle Proper Dih. Improper Dih. LJ-14
> 3.30312e+03 1.22047e+04 6.95879e+04 6.55239e+02 1.88651e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.26345e+05 7.77640e+05 -3.36842e+04 -5.58600e+06 1.46894e+04
> Potential Kinetic En. Total Energy Conserved En. Temperature
> -4.49639e+06 5.57315e+03 -4.49082e+06 -3.56022e+06 2.36895e+00
> Pres. DC (bar) Pressure (bar) Constr. rmsd
> -1.86887e+02 -1.43160e+03 2.50109e-06
> -
>
> And when I used gmx energy to generate temp curve, I got this at the 
> beginning:
>
> 0.00 300.605164 300.543854 300.611908
> 1.00 5.131036 3.108571 5.354491
> 2.00 2.263988 1.550216 2.342851
> 3.00 2.368947 1.869242 2.424157
> 4.00 2.709096 2.333785 2.750562
> 5.00 3.236674 3.030164 3.259491
> 6.00 3.733118 3.523592 3.756267
> 7.00 4.282474 3.992255 4.314539
> 8.00 4.829560 4.523222 4.863406
> 9.00 5.418922 5.164090 5.447078
>
>
> Also I noticed a shrink in the water box after NVT, and it expands to the 
> usual at the start of NPT, is the shrink realted to this?

Possibly. If you tell the system it's at 300 K, but then force the 
thermostat to try to damp the velocities down to zero, you're going to 
get weird physical behavior.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.

[gmx-users] simulated annealing

[Ahmed Mashaly]

Hi
If I want to heat the system from 0 to 300K gradually in NVT via simulated 
annealing
the ref-t and gen-temp should be 0 or 300?
 Kind Regards,Ahmed

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[gmx-users] PBC

[Ahmed Mashaly]

Hi
If I want to use gmx trjconv to recenter the protein in xtc file, the reference 
(-s) .tpr should be the one I used in simulation (md.tpr) or I can use the 
first one (em.tpr) without a difference?

This is because the protein has jumped after em step, and if I have to use 
md.tpr as reference for md.xtc, I will have to recenter it after every step of 
em, nvt, npt
Kind Regards,Ahmed 

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[gmx-users] RMS for many trajectories

[Ahmed Mashaly]

Hi
Is there a way to calculate rms for 20 trajectories without joining them? Kind 
Regards,Ahmed

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Re: [gmx-users] Running long MD simulation

[Ahmed Mashaly]

Sorry, I see the point of ndx now ... I thought there was no default group for 
water_and_ions.
However, the second question is still running through my head Kind 
Regards,Ahmed 



  From: Ahmed Mashaly <mashaly_1...@yahoo.com>
 To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> 
 Sent: Thursday, February 8, 2018 9:49 AM
 Subject: Re: [gmx-users] Running long MD simulation
   
And why don't we modify the .mdp file to be protein_and_JZ4 as the same way you 
did for water_and_ions instead of making a new index for the list protein_JZ4?
And why do we have some groups duplicated in the default index? for example in 
the tut, JZ4 was No. 13 and 19, Ion and CL the same, water and SOL the same! 
Kind Regards,Ahmed Mashaly



  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Sunday, February 4, 2018 4:02 PM
 Subject: Re: [gmx-users] Running long MD simulation
  


On 2/4/18 9:57 AM, Ahmed Mashaly wrote:
> And the index file? what is the point of inserting them as input for NPT and 
> MD? They should be for the whole system, not certain groups, right? Kind 
> Regards,Ahmed

Please consult basic tutorials that explain the purpose of these files 
for thermostatting, energygrps, etc.

-Justin

>
>
>        From: Justin Lemkul <jalem...@vt.edu>
>  To: gmx-us...@gromacs.org
>  Sent: Sunday, February 4, 2018 4:20 PM
>  Subject: Re: [gmx-users] Running long MD simulation
>    
>
>
> On 2/4/18 9:15 AM, Ahmed Mashaly wrote:
>> Thanks Justin.
>>
>> I found this one:
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118282.html
>>
>> Another question I have about using cpt
>>
>> I know checkpoint is important for continuing simulation, but I didn't know 
>> that we have to use it also from nvt output to npt input and from npt output 
>> to md input ... I was just using the output .gro as input for the next step 
>> ... Is this a fatal mistake?
> Checkpoint files are essential for exact continuations. Without them,
> you lose thermodynamic state information, precise velocities, etc.
> Always use a checkpoint.
>
>> If I have to use it then I can use it with grompp -t prev_checkpoint.cpt or 
>> with mdrun -cpi prev_checkpoint.cpt ... Would it be the same result?
>>    
> You only need to invoke grompp if changing something about the system -
> output settings, ensemble, use of restraints, etc. Otherwise, just
> extend via convert-tpr and mdrun -cpi.
>
> -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] Running long MD simulation

[Ahmed Mashaly]

And why don't we modify the .mdp file to be protein_and_JZ4 as the same way you 
did for water_and_ions instead of making a new index for the list protein_JZ4?
And why do we have some groups duplicated in the default index? for example in 
the tut, JZ4 was No. 13 and 19, Ion and CL the same, water and SOL the same! 
Kind Regards,Ahmed Mashaly



  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Sunday, February 4, 2018 4:02 PM
 Subject: Re: [gmx-users] Running long MD simulation
   


On 2/4/18 9:57 AM, Ahmed Mashaly wrote:
> And the index file? what is the point of inserting them as input for NPT and 
> MD? They should be for the whole system, not certain groups, right? Kind 
> Regards,Ahmed

Please consult basic tutorials that explain the purpose of these files 
for thermostatting, energygrps, etc.

-Justin

>
>
>        From: Justin Lemkul <jalem...@vt.edu>
>  To: gmx-us...@gromacs.org
>  Sent: Sunday, February 4, 2018 4:20 PM
>  Subject: Re: [gmx-users] Running long MD simulation
>    
>
>
> On 2/4/18 9:15 AM, Ahmed Mashaly wrote:
>> Thanks Justin.
>>
>> I found this one:
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118282.html
>>
>> Another question I have about using cpt
>>
>> I know checkpoint is important for continuing simulation, but I didn't know 
>> that we have to use it also from nvt output to npt input and from npt output 
>> to md input ... I was just using the output .gro as input for the next step 
>> ... Is this a fatal mistake?
> Checkpoint files are essential for exact continuations. Without them,
> you lose thermodynamic state information, precise velocities, etc.
> Always use a checkpoint.
>
>> If I have to use it then I can use it with grompp -t prev_checkpoint.cpt or 
>> with mdrun -cpi prev_checkpoint.cpt ... Would it be the same result?
>>    
> You only need to invoke grompp if changing something about the system -
> output settings, ensemble, use of restraints, etc. Otherwise, just
> extend via convert-tpr and mdrun -cpi.
>
> -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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[gmx-users] Octahedral minimization problem

[Ahmed Mashaly]

Hi

Two solvated systems with amber were converted to .gro with acpype. one is box 
the other is octahedral


The box can be minimized in cluster with this em.mdp file


integrator = steep 
emtol = 100.0 
emstep = 0.01 
nsteps = 5 

nstlist = 1 
cutoff-scheme 
ns_type = grid 
coulombtype = PME 
rcoulomb = 1.0
rvdw = 1.0 
pbc = xyz 


The box can be minimized, but at the end I had 

Steepest Descents converged to Fmax < 100 in 2706 steps
Potential Energy = -2.7121270e+06
Maximum force = 9.3153786e+01 on atom 163971
Norm of force = 1.7101741e+00
Simulation ended prematurely, no performance report will be written.

as I understood from other messages in archive this premature is not a problem 
as it ends with good pot energy and max force

While in case of octahedral, I got this:

Steepest Descents:
Tolerance (Fmax) = 1.0e+02
Number of steps = 5
Step= 0, Dmax= 1.0e-03 nm, Epot= 8.27123e+15 Fmax= 1.65730e+17, atom= 103876
Step= 1, Dmax= 1.0e-03 nm, Epot= 4.22395e+15 Fmax= 6.54268e+16, atom= 103876
Step= 2, Dmax= 1.2e-03 nm, Epot= 1.96761e+15 Fmax= 2.32216e+16, atom= 103876
Step= 3, Dmax= 1.4e-03 nm, Epot= 8.64595e+14 Fmax= 7.37977e+15, atom= 103876
Step= 4, Dmax= 1.7e-03 nm, Epot= 3.77835e+14 Fmax= 2.09380e+15, atom= 103876
Step= 5, Dmax= 2.1e-03 nm, Epot= 1.49451e+14 Fmax= 5.29119e+14, atom= 103876
Step= 6, Dmax= 2.5e-03 nm, Epot= 5.37730e+13 Fmax= 1.41647e+14, atom= 34363
Step= 7, Dmax= 3.0e-03 nm, Epot= 1.82718e+13 Fmax= 3.59846e+13, atom= 199780
Step= 8, Dmax= 3.6e-03 nm, Epot= 6.05245e+12 Fmax= 7.92220e+12, atom= 134203
Step= 9, Dmax= 4.3e-03 nm, Epot= 1.72087e+12 Fmax= 1.62912e+12, atom= 72328
Step= 10, Dmax= 5.2e-03 nm, Epot= 4.91989e+11 Fmax= 3.31401e+11, atom= 106294
Step= 11, Dmax= 6.2e-03 nm, Epot= 1.59698e+11 Fmax= 7.11892e+10, atom= 136966
Step= 12, Dmax= 7.4e-03 nm, Epot= 5.16370e+10 Fmax= 1.55656e+10, atom= 14985
Step= 13, Dmax= 8.9e-03 nm, Epot= 1.66064e+10 Fmax= 6.35415e+09, atom= 14986
Step= 14, Dmax= 1.1e-02 nm, Epot= 8.82293e+09 Fmax= 3.16163e+09, atom= 14985
Step= 15, Dmax= 1.3e-02 nm, Epot= 4.84420e+09 Fmax= 8.10766e+08, atom= 14986
Step= 16, Dmax= 1.5e-02 nm, Epot= 1.68188e+09 Fmax= 2.50214e+08, atom= 14985
Step= 17, Dmax= 1.8e-02 nm, Epot= 7.22330e+08 Fmax= 3.72832e+07, atom= 14986
Step= 18, Dmax= 2.2e-02 nm, Epot= 1.55106e+08 Fmax= 8.66899e+06, atom= 17209
Step= 19, Dmax= 2.7e-02 nm, Epot= 7.04906e+07 Fmax= 4.10104e+06, atom= 152596
Step= 20, Dmax= 3.2e-02 nm, Epot= 4.15026e+07 Fmax= 1.23764e+06, atom= 152596
Step= 21, Dmax= 3.8e-02 nm, Epot= 1.95151e+07 Fmax= 8.10870e+06, atom= 164668
Step= 22, Dmax= 4.6e-02 nm, Epot= 1.78878e+07 Fmax= 9.02967e+05, atom= 164668
Step= 23, Dmax= 5.5e-02 nm, Epot= 1.14131e+07 Fmax= 5.10415e+06, atom= 164668

step 24: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 24: One or more water molecules 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
Fatal error in MPI_Sendrecv: Message truncated, error stack:
MPI_Sendrecv(259).: MPI_Sendrecv(sbuf=0x7ffed5bfe230, scount=8, 
MPI_BYTE, dest=8, stag=0, rbuf=0x7ffed5bfe238, rcount=8, MPI_BYTE, src=6, 
rtag=0, MPI_COMM_WORLD, status=0x7ffed5bfdf90) failed
MPIDI_CH3U_Receive_data_found(131): Message from rank 6 and tag 0 truncated; 
17016 bytes received but buffer size is 8


>From the checked archive I know people had similar problems will be related to 
>topology and atomic clashes, but I don`t have any and some meaningless pdb 
>files were produced with the name of this step. but when I tried on my laptop, 
>the same water error appeared, but the minimization process continued with pdb 
>(s) created and at the end I got this with gro file and everything and this 
>log:


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)

Steepest Descents converged to machine precision in 13158 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -3.8879410e+06
Maximum force = 1.8154966e+03 on atom 21160
Norm of force = 5.8444543e+00

Simulation ended prematurely, no performance report will be written.



Later when I tried to run it in the cluster, but with only one cpu instead of 
many (48, 10, 5 were tried and got the same error), but with only 

Re: [gmx-users] Running long MD simulation

[Ahmed Mashaly]

And the index file? what is the point of inserting them as input for NPT and 
MD? They should be for the whole system, not certain groups, right? Kind 
Regards,Ahmed



  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Sunday, February 4, 2018 4:20 PM
 Subject: Re: [gmx-users] Running long MD simulation
   


On 2/4/18 9:15 AM, Ahmed Mashaly wrote:
> Thanks Justin.
>
> I found this one:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118282.html
>
> Another question I have about using cpt
>
> I know checkpoint is important for continuing simulation, but I didn't know 
> that we have to use it also from nvt output to npt input and from npt output 
> to md input ... I was just using the output .gro as input for the next step 
> ... Is this a fatal mistake?

Checkpoint files are essential for exact continuations. Without them, 
you lose thermodynamic state information, precise velocities, etc. 
Always use a checkpoint.

> If I have to use it then I can use it with grompp -t prev_checkpoint.cpt or 
> with mdrun -cpi prev_checkpoint.cpt ... Would it be the same result?
>  

You only need to invoke grompp if changing something about the system - 
output settings, ensemble, use of restraints, etc. Otherwise, just 
extend via convert-tpr and mdrun -cpi.

-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] Running long MD simulation

[Ahmed Mashaly]

Thanks Justin.

I found this one:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118282.html

Another question I have about using cpt

I know checkpoint is important for continuing simulation, but I didn't know 
that we have to use it also from nvt output to npt input and from npt output to 
md input ... I was just using the output .gro as input for the next step ... Is 
this a fatal mistake?

If I have to use it then I can use it with grompp -t prev_checkpoint.cpt or 
with mdrun -cpi prev_checkpoint.cpt ... Would it be the same result?
 

Kind Regards,
Ahmed 






From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org 
Sent: Friday, February 2, 2018 5:27 PM
Subject: Re: [gmx-users] Running long MD simulation






On 2/1/18 12:45 PM, Ahmed Mashaly wrote:
> Hi
> I want to run a long MD 200 ns, but I want the outputs of every 5 ns to be 
> saved separately ... Is there a way or a script to do this? Kind Regards,Ahmed
>
It should be very simple with a bash loop and making use of mdrun 
-noappend so you avoid naming clashes. People have done this before and 
posted to the list; just Google within the archive.

-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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[gmx-users] Running long MD simulation

[Ahmed Mashaly]

Hi
I want to run a long MD 200 ns, but I want the outputs of every 5 ns to be 
saved separately ... Is there a way or a script to do this? Kind Regards,Ahmed

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Re: [gmx-users] Grompp warning about topology constrains

[Ahmed Mashaly]

Thanks Justin Kind Regards,Ahmed Mashaly



  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Tuesday, January 30, 2018 6:00 PM
 Subject: Re: [gmx-users] Grompp warning about topology constrains
   


On 1/30/18 5:46 AM, Ahmed Mashaly wrote:
>
> Thanks Justin ... The topology seems fine to me
>
> The inputs are in this link incase of the text is messed again
> https://drive.google.com/open?id=13DzlUl0rLoJBfr_oPf9tLPknAsRNJpuR
>
>
>
> title = NVT
> define = -DPOSRES ;
>
> ; Run parameters
> integrator = md
> dt = 0.002
> nsteps = 25
>
> ; Output control
> nstlog = 500
> nstxout = 500
> nstvout = 500
> nstfout = 500
> nstcalcenergy = 10
> nstenergy = 500
>
> ; Bond parameters
> continuation = no
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter = 2
> lincs_order = 4
> shake-tol        = 1e-05
>
> ; Neighborsearching
> cutoff-scheme = Verlet
> ns_type = grid
> nstlist = 10
> rlist = 1.0
> rvdw = 1.0
> vdwtype = Cut-off
> rcoulomb = 1.0
>
> ; Electrostatics
> coulombtype = pme
> pme_order = 4
> fourierspacing = 0.16
>
> ; Temperature coupling
> tcoupl = V-rescale
> tc_grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 300 300
>
> ; Pressure coupling
> pcoupl = no
>
> ; Periodic boundary conditions
> pbc = xyz
>
> ; Dispersion correction
> DispCorr = EnerPres
>
> ;
> gen_vel = yes
> gen_temp = 300
> gen_seed = -1
>
>
>
>
>
> The last lines of toplogy:

As I said before, the line numbers here and their contents are irrelevant.

The error message and its solution are quite clear. You have at least 
one angle between some atoms i-j-k, in which the masses of atoms i and k 
differ by at least a factor of 13. In this instance, you shouldn't be 
constraining all bonds. Set constraints = h-bonds and move ahead. The 
only force field that I know of that requires all bonds to be 
constrained is GROMOS, all others normally only constrain bonds to H.

-Justin

> 79101 [ moleculetype ]
> 79102 ; Name nrexcl
> 79103 SOL 3
> 79104
> 79105 [ atoms ]
> 79106 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 79107 ; residue 1 WAT rtp WAT q 0.0
> 79108 1 OW 1 SOL OW 1 -0.834000 16. ; qtot -0.8340
> 79109 2 HW 1 SOL HW1 2 0.417000 1.0080 ; qtot -0.4170
> 79110 3 HW 1 SOL HW2 3 0.417000 1.0080 ; qtot 0.
> 79111
> 79112 #ifdef FLEXIBLE
> 79113
> 79114 [ bonds ]
> 79115 ; ai aj funct c0 c1 c2 c3
> 79116 2 3 1 0.15136 462750.40
> 79117 1 2 1 0.09572 462750.40
> 79118 1 3 1 0.09572 462750.40
> 79119
> 79120
> 79121 #else
> 79122
> 79123 [ settles ]
> 79124 ; i funct doh dhh
> 79125 1 1 0.09572 0.15136
> 79126
> 79127 #endif
> 79128
> 79129 [ exclusions ]
> 79130 1 2 3
> 79131 2 1 3
> 79132 3 1 2
> 79133
> 79134 [ system ]
> 79135 ; Name
> 79136 Generic title
> 79137
> 79138 [ molecules ]
> 79139 ; Compound #mols
> 79140 system1 1
> 79141 system2 1
> 79142 system1 1
> 79143 system2 1
> 79144 system1 1
> 79145 system2 1
> 79146 NA 3
> 79147 SOL 49664
>
>
>
>
>  
> Kind Regards,
> Ahmed
>
>
>
>
>
> 
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Sent: Tuesday, January 30, 2018 2:14 AM
> Subject: Re: [gmx-users] Grompp warning about topology constrains
>
>
>
>
>
> On 1/29/18 11:03 AM, Ahmed Mashaly wrote:
>> Hi,
>> I have set up my parameters with tleap, converted to gromacs with Acpype, 
>> did the minimization.
>>
>>
>> For NVT, when I use grompp, this warning appears:
>> WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of 
>> an angle, connected by constraints and  with masses that differ by more than 
>> a factor of 13. This means that  there are likely dynamic modes that are 
>> only very weakly coupled. To  ensure good equipartitioning, you need to 
>> either not use constraints on  all bonds (but, if possible, only on bonds 
>> involving hydrogens) or use  integrator = sd or decrease one or more 
>> tolerances:  verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS 
>> order >=  4 or SHAKE tolerance <= 1e-05
>>
>> But in .top file there in this line (the last one) there is no such a thing.
> The error appears at the end of topology parsing, so it reports the last
> line as being the source, but that's not correct. It's just a reflection
> of the fact that you're doing something unstable somewhere in the topology.
>
>> It worked when I changed the integrator to sd or when I c

Re: [gmx-users] Grompp warning about topology constrains

[Ahmed Mashaly]

Thanks Justin ... The topology seems fine to me

The inputs are in this link incase of the text is messed again
https://drive.google.com/open?id=13DzlUl0rLoJBfr_oPf9tLPknAsRNJpuR



title = NVT
define = -DPOSRES ;

; Run parameters
integrator = md
dt = 0.002
nsteps = 25

; Output control
nstlog = 500
nstxout = 500
nstvout = 500
nstfout = 500
nstcalcenergy = 10 
nstenergy = 500

; Bond parameters
continuation = no 
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 2
lincs_order = 4
shake-tol = 1e-05 

; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid
nstlist = 10
rlist = 1.0
rvdw = 1.0
vdwtype = Cut-off
rcoulomb = 1.0

; Electrostatics
coulombtype = pme
pme_order = 4
fourierspacing = 0.16

; Temperature coupling
tcoupl = V-rescale
tc_grps = Protein Non-Protein 
tau_t = 0.1 0.1
ref_t = 300 300

; Pressure coupling
pcoupl = no

; Periodic boundary conditions
pbc = xyz

; Dispersion correction
DispCorr = EnerPres

;
gen_vel = yes
gen_temp = 300
gen_seed = -1  





The last lines of toplogy:

79101 [ moleculetype ]
79102 ; Name nrexcl
79103 SOL 3
79104 
79105 [ atoms ]
79106 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
79107 ; residue 1 WAT rtp WAT q 0.0
79108 1 OW 1 SOL OW 1 -0.834000 16. ; qtot -0.8340
79109 2 HW 1 SOL HW1 2 0.417000 1.0080 ; qtot -0.4170
79110 3 HW 1 SOL HW2 3 0.417000 1.0080 ; qtot 0.
79111 
79112 #ifdef FLEXIBLE
79113 
79114 [ bonds ]
79115 ; ai aj funct c0 c1 c2 c3
79116 2 3 1 0.15136 462750.40
79117 1 2 1 0.09572 462750.40
79118 1 3 1 0.09572 462750.40
79119 
79120 
79121 #else
79122 
79123 [ settles ]
79124 ; i funct doh dhh
79125 1 1 0.09572 0.15136
79126 
79127 #endif
79128 
79129 [ exclusions ]
79130 1 2 3
79131 2 1 3
79132 3 1 2
79133 
79134 [ system ]
79135 ; Name
79136 Generic title
79137 
79138 [ molecules ]
79139 ; Compound #mols
79140 system1 1
79141 system2 1
79142 system1 1
79143 system2 1
79144 system1 1
79145 system2 1
79146 NA 3
79147 SOL 49664




 
Kind Regards,
Ahmed






From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org 
Sent: Tuesday, January 30, 2018 2:14 AM
Subject: Re: [gmx-users] Grompp warning about topology constrains





On 1/29/18 11:03 AM, Ahmed Mashaly wrote:
> Hi,
> I have set up my parameters with tleap, converted to gromacs with Acpype, did 
> the minimization.
>
>
> For NVT, when I use grompp, this warning appears:
> WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of an 
> angle, connected by constraints and  with masses that differ by more than a 
> factor of 13. This means that  there are likely dynamic modes that are only 
> very weakly coupled. To  ensure good equipartitioning, you need to either not 
> use constraints on  all bonds (but, if possible, only on bonds involving 
> hydrogens) or use  integrator = sd or decrease one or more tolerances:  
> verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=  4 
> or SHAKE tolerance <= 1e-05
>
> But in .top file there in this line (the last one) there is no such a thing.

The error appears at the end of topology parsing, so it reports the last 
line as being the source, but that's not correct. It's just a reflection 
of the fact that you're doing something unstable somewhere in the topology.

> It worked when I changed the integrator to sd or when I changed the 
> constraints to only h-bonds and not with LINCS iterations >= 2, LINCS order 
> >= 4 or SHAKE tolerance <= 1e-05
>
>
> I even deleteddefine  = -DPOSRES
> from the .mdp file and got the same warning

Position restraints have nothing to do with bond constraints.

The text below is basically unintelligible. Please use proper line 
wrapping in your email client.

-Justin


>
> this is my input file:itle   = NVT define  = 
> -DPOSRES ; Run parametersintegrator  = md   dt
>   = 0.002nsteps  = 25   ; Output controlnstlog
>   = 500 nstxout = 500nstvout  
>= 500 nstfout = 500 nstcalcenergy   = 10  
> nstenergy   = 500; Bond parameterscontinuation= 
> no   constraint_algorithm= lincs   constraints = 
> all-bonds lincs_iter  = 2   lincs_order = 
> 4  shake-tol = 1e-05  ; Neighborsearchingcutoff-scheme   = 
> Verletns_type = grid   nstlist = 10   
>  rlist   = 1.0rvdw= 
> 1.0vdwtype = Cut-offrcoulomb= 1.0 
>; Electrostaticscoulombtype = pme  
   pme_order   = 4  

[gmx-users] emtol value

[Ahmed Mashaly]

Hi,
What should be the emtol value for big proteins and system? speaking about 
+1500 residue and +50k water molecule. 
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[gmx-users] Grompp warning about topology constrains

[Ahmed Mashaly]

Hi,
I have set up my parameters with tleap, converted to gromacs with Acpype, did 
the minimization.


For NVT, when I use grompp, this warning appears:
WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of an 
angle, connected by constraints and  with masses that differ by more than a 
factor of 13. This means that  there are likely dynamic modes that are only 
very weakly coupled. To  ensure good equipartitioning, you need to either not 
use constraints on  all bonds (but, if possible, only on bonds involving 
hydrogens) or use  integrator = sd or decrease one or more tolerances:  
verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=  4 or 
SHAKE tolerance <= 1e-05

But in .top file there in this line (the last one) there is no such a thing.

It worked when I changed the integrator to sd or when I changed the constraints 
to only h-bonds and not with LINCS iterations >= 2, LINCS order >= 4 or SHAKE 
tolerance <= 1e-05


I even deleteddefine                  = -DPOSRES
from the .mdp file and got the same warning


this is my input file:itle                   = NVT define                  = 
-DPOSRES ; Run parametersintegrator              = md       dt                  
    = 0.002    nsteps                  = 25   ; Output controlnstlog        
          = 500     nstxout                 = 500    nstvout                 = 
500     nstfout                 = 500     nstcalcenergy           = 10  
nstenergy               = 500    ; Bond parameterscontinuation            = no  
     constraint_algorithm    = lincs       constraints             = all-bonds  
   lincs_iter              = 2           lincs_order             = 4          
shake-tol = 1e-05  ; Neighborsearchingcutoff-scheme           = Verletns_type   
              = grid           nstlist                 = 10            rlist    
               = 1.0            rvdw                    = 1.0            
vdwtype                 = Cut-offrcoulomb                = 1.0            ; 
Electrostaticscoulombtype             = pme            pme_order               
= 4              fourierspacing          = 0.16           
; Temperature couplingtcoupl                  = V-rescaletc_grps                
 = Protein Non-Protein tau_t                   = 0.1    0.1ref_t                
   = 300    300
; Pressure couplingpcoupl                  = no        ; Periodic boundary 
conditionspbc                     = xyz       ; Dispersion correctionDispCorr   
             = EnerPres  ;gen_vel                 = yes       gen_temp          
      = 300       gen_seed                = -1  



And these are the last lines of .top with line numbers (starting 79101)  79101 
[ moleculetype ]  79102 ; Name            nrexcl  79103 SOL          3  79104   
79105 [ atoms ]  79106 ;   nr       type  resnr residue  atom   cgnr    charge  
     mass  typeB    chargeB      massB  79107 ; residue    1 WAT rtp WAT q 0.0  
79108     1         OW      1    SOL     OW      1  -0.834000    16.   ; 
qtot -0.8340  79109     2         HW      1    SOL    HW1      2   0.417000     
1.0080   ; qtot -0.4170  79110     3         HW      1    SOL    HW2      3   
0.417000     1.0080   ; qtot 0.  79111   79112 #ifdef FLEXIBLE  79113   
79114 [ bonds ]  79115 ;    ai     aj funct         c0         c1         c2    
     c3  79116       2      3     1   0.15136 462750.40  79117       1      
2     1   0.09572 462750.40  79118       1      3     1   0.09572 
462750.40  79119   79120   79121 #else  79122   79123 [ settles ]  79124 ; 
i     funct   doh     dhh  79125 1     1   0.09572   0.15136  79126   79127 
#endif  79128   79129 [ exclusions ]  79130 1  2  3  79131 2  1  3  79132 3  1  
2  79133   79134 [ system ]  79135 ; Name  79136 Generic title  79137   79138 [ 
molecules ]  79139 ; Compound       #mols  79140 system1              1  79141 
system2              1  79142 system1              1  79143 system2             
 1  79144 system1              1  79145 system2              1  79146 NA        
           3  79147 SOL              49664
Thanks,Ahmed
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[gmx-users] Recentering a protein

[Ahmed Mashaly]

Hi
I am new to gromacs (using v. 2016.4) and need to check the following steps for 
my system.
01. I have prepared the system with Amber 14, minimized, heated to 300K, 
equilibrated 02. Then I used Acpype to convert the amber top and equilibrated 
rst file to gromacs .top and .gro files03. Changing Na+ to NA and WAT to SOL 
and H and O of water to HW1 HW2 and OW04. Doing a CG minimization again with 
gromacs.05. Doing a NPT with gromacs06. Running MD simulation with gromacs.
Is this procedure correct or do I need any modification?
In Amber we used to run MD for 5 ns, then recenter then relaunch from the last 
rst file. The same case will be with gromacs.Is there a script I can find to 
recenter and relunch the process automatically?

Another thing after doing the minimization, I cannot recenter the protein by 
trjconv command gmx trjconv -f em.gro -s em.tpr -o em_1.gro -center -pbc mol 
-ur compact>> selecting 1 to center protein>> selecting 0 to get the whole 
system output
https://drive.google.com/open?id=13lGcj52NpteRPTBHFJOKlXZ9dUliezqd
In this link you have The acp.gro and acp.top file produced from Acpype with 
modifications to Na and watermdp files for Min, NPT, MD, please check themAnd 
the em.gro the file produced after minimization which cannot be centered
Many thanks
Kind Regards,Ahmed 

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