Re: [gmx-users] Fwd: geometry optimization of metalloenzyme

[Justin Lemkul]

On 4/9/20 4:25 PM, Nadia Elghobashi-Meinhardt wrote:

Thank you, Justin.
I am still struggling with constraints.
I am trying to use "freezegrps" and "freezedim"
to run an NVT equilibration.
However, when I try to build the binary using my optimized structure, I get
either "Segmentation fault" or the following error:
"free(): invalid next size (fast)
Aborted"
What do these messages indicate? Problem in memory allocation?


All of this is probably a downstream effect of a simulation that is 
unstable and crashed.


Freezing is totally artificial and I strongly discourage using it. The 
crash may be due to failure to use energygrp_exclusions when freezing or 
due to intrinsic instability of the system that even freezing cannot 
overcome.


-Justin


On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul  wrote:



On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote:

Hello everyone,

I am trying to minimize the potential energy of a
metalloenzyme containing Ni and Fe atoms.
What is the best way to constrain (fix?) the position of the active site
atoms
during the geometry optimization?
I have tried introducing bonds with relatively high force constants and
alternatively, tried introducing a [constraints] section,
but the atoms are still not staying put.

Bonds or constraints will maintain distances between atoms (relative
position) but not absolute position.


Or should one use extra position restraints?

If the absolute position matters, yes. I would think the approach of
adding restraints or constraints between atoms would be more meaningful
given that preserving coordination geometry is often the defect in MM
treatment of transition metals.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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==

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Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

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[gmx-users] Fwd: Fwd: geometry optimization of metalloenzyme

[Nadia Elghobashi-Meinhardt]

Thank you, Justin.
I am still struggling with constraints.
I am trying to use "*freezegrps*" and "*freezedim*"
to run an NVT equilibration of a structure (successfully
geometry-optimized using freezegrps).

However, when I try to build the binary using my optimized structure, I get
either "Segmentation fault" or the following error:
"free(): invalid next size (fast)
Aborted"
These messages seem to indicate a memory allocation problem,
but I cannot isolate the problem.
I am not sure of the correct combination of constraint (lincs) keywords in
the nvt input, especially how to combine these with the
freezegrps/freezedim commands.
Do anybody have any tips or helpful examples?


On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul  wrote:

>
>
> On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote:
> > Hello everyone,
> >
> > I am trying to minimize the potential energy of a
> > metalloenzyme containing Ni and Fe atoms.
> > What is the best way to constrain (fix?) the position of the active site
> > atoms
> > during the geometry optimization?
> > I have tried introducing bonds with relatively high force constants and
> > alternatively, tried introducing a [constraints] section,
> > but the atoms are still not staying put.
>
> Bonds or constraints will maintain distances between atoms (relative
> position) but not absolute position.
>
> > Or should one use extra position restraints?
>
> If the absolute position matters, yes. I would think the approach of
> adding restraints or constraints between atoms would be more meaningful
> given that preserving coordination geometry is often the defect in MM
> treatment of transition metals.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Fwd: geometry optimization of metalloenzyme

[Nadia Elghobashi-Meinhardt]

Thank you, Justin.
I am still struggling with constraints.
I am trying to use "freezegrps" and "freezedim"
to run an NVT equilibration.
However, when I try to build the binary using my optimized structure, I get
either "Segmentation fault" or the following error:
"free(): invalid next size (fast)
Aborted"
What do these messages indicate? Problem in memory allocation?

On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul  wrote:

>
>
> On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote:
> > Hello everyone,
> >
> > I am trying to minimize the potential energy of a
> > metalloenzyme containing Ni and Fe atoms.
> > What is the best way to constrain (fix?) the position of the active site
> > atoms
> > during the geometry optimization?
> > I have tried introducing bonds with relatively high force constants and
> > alternatively, tried introducing a [constraints] section,
> > but the atoms are still not staying put.
>
> Bonds or constraints will maintain distances between atoms (relative
> position) but not absolute position.
>
> > Or should one use extra position restraints?
>
> If the absolute position matters, yes. I would think the approach of
> adding restraints or constraints between atoms would be more meaningful
> given that preserving coordination geometry is often the defect in MM
> treatment of transition metals.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
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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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[gmx-users] Fwd: no atom pairs for dispersion correction

[Sadaf Rani]

Dear Gromacs users
I am running an MD simulation of the protein-ligand complex. At the start
of the production run, I am getting this warning. What does it mean and how
should I fix it?

*WARNING: There are no atom pairs for dispersion correction*

Thanks in advance.

Sadaf
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Re: [gmx-users] Fwd: geometry optimization of metalloenzyme

[Justin Lemkul]

On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote:

Hello everyone,

I am trying to minimize the potential energy of a
metalloenzyme containing Ni and Fe atoms.
What is the best way to constrain (fix?) the position of the active site
atoms
during the geometry optimization?
I have tried introducing bonds with relatively high force constants and
alternatively, tried introducing a [constraints] section,
but the atoms are still not staying put.


Bonds or constraints will maintain distances between atoms (relative 
position) but not absolute position.



Or should one use extra position restraints?


If the absolute position matters, yes. I would think the approach of 
adding restraints or constraints between atoms would be more meaningful 
given that preserving coordination geometry is often the defect in MM 
treatment of transition metals.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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[gmx-users] Fwd: geometry optimization of metalloenzyme

[Nadia Elghobashi-Meinhardt]

Hello everyone,

I am trying to minimize the potential energy of a
metalloenzyme containing Ni and Fe atoms.
What is the best way to constrain (fix?) the position of the active site
atoms
during the geometry optimization?
I have tried introducing bonds with relatively high force constants and
alternatively, tried introducing a [constraints] section,
but the atoms are still not staying put.
Or should one use extra position restraints?

Any tips are welcome!
Thank you.
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Re: [gmx-users] Fwd: Reproducibility of a PMF plot

[André Farias de Moura]

Dear Alex,

in a nutshell: yes, convergence might not have been achieved even if the
estimated error bars seem small.

maybe this reference might be helpful:

https://doi.org/10.1016/j.bbamem.2016.03.006

best,

Andre

On Tue, Mar 17, 2020 at 2:14 PM Alex  wrote:

> Any comment, please?
>
> Thank you,
> Alex
>
> -- Forwarded message -
> From: Alex 
> Date: Sun, Mar 15, 2020 at 8:16 PM
> Subject: Reproducibility of a PMF plot
> To: 
>
>
> Dear all,
>
> Of course it is always good to prove that a MD simulation is reproducible
> by repeating several replicas of a simulation and then average over the
> quantity of interest, specially for a publishable result.
> I wonder if that also is necessary for a potential of mean force (PMF)
> calculation using umbrella sampling in which the bootstrap analysis is
> performed to calculate the standard deviation?
> Or for an alchemical free energy calculation where the e.g. the block
> averaging is used?
>
> Regards,
> Alex
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>


-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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[gmx-users] Fwd: Reproducibility of a PMF plot

[Alex]

Any comment, please?

Thank you,
Alex

-- Forwarded message -
From: Alex 
Date: Sun, Mar 15, 2020 at 8:16 PM
Subject: Reproducibility of a PMF plot
To: 


Dear all,

Of course it is always good to prove that a MD simulation is reproducible
by repeating several replicas of a simulation and then average over the
quantity of interest, specially for a publishable result.
I wonder if that also is necessary for a potential of mean force (PMF)
calculation using umbrella sampling in which the bootstrap analysis is
performed to calculate the standard deviation?
Or for an alchemical free energy calculation where the e.g. the block
averaging is used?

Regards,
Alex
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[gmx-users] Fwd: Problems with Non-equilibrium MD

[Jun Zhou]

Hi all,

I am using non-equilibrium MD to calculate the viscosity of the liquid by
applying a shear on xy direction. My problem is that when I observe the
trajectory of the simulation, I find only the box deformed and particles
did not change correspondingly, as shown in the attached image.

I also attached my mdp file, can anyone give me some suggestions? Thanks.

Regards

-- 
*Jun ZHOU*
Postgraduate Student ,
Room 117, Building 36
Department of Civil Engineering,
Monash University,
Victoria 3800, Australia.
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Re: [gmx-users] Fwd: Problems with Non-equilibrium MD

[Benson Muite]

Hi Jun,
Can you add a link to your image online rather than attaching it?
Benson



On Mon, Mar 16, 2020, at 10:25 AM, Jun Zhou wrote:
> Hi all,
> 
> I am using non-equilibrium MD to calculate the viscosity of the liquid by
> applying a shear on xy direction. My problem is that when I observe the
> trajectory of the simulation, I find only the box deformed and particles
> did not change correspondingly, as shown in the attached image.
> 
> I also attached my mdp file, can anyone give me some suggestions? Thanks.
> 
> Regards
> 
> -- 
> *Jun ZHOU*
> Postgraduate Student ,
> Room 117, Building 36
> Department of Civil Engineering,
> Monash University,
> Victoria 3800, Australia.
> 
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[gmx-users] Fwd: Force field for urea and urea-TMAO mixture

[ISHRAT JAHAN]

Dear all,
I want to do MD simulation of protein in urea and urea-TMAO mixture. Can
you suggest to me which force field would be better for urea and urea tmao
mixture? Is the Kast-2016 TMAO model is compatible with the gromos54a5
force field as I have done the simulation of protein with this force field?
Any suggestions regarding this will be highly appreciated.
Thank you
Regards


-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh
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[gmx-users] Fwd: regarding dihedral restraints

[Sadaf Rani]

Dear Gromacs users
I am restraining three dihedral angles between atoms of two
different residues. when I measure it using the following command:-

gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of
trans.xvg

I am getting one of my dihedrals graphs as mentioned in the link.
https://www.dropbox.com/sh/1ff45is9412dld4/AACDXjV0T47P01RgCJ1Baccca?dl=0
My dihedral angles have a multiplicity of 1 as mentioned below:-
[ dihedral_restraints ]
;   aiajakal   type   phiA dphiAfcA phiBdphiB
  fcB
72743133   1 146.72 0.0 0   146.72 0.0
41.840
7574 3127   1 173.10 0.0 0   173.10 0.0   41.840
7574 3125   1 158.21 0.0 0   158.21 0.0   41.840

 However, in gromacs manual, I read this:-


*Counting transitions only works for dihedrals with multiplicity 3*
Am I doing something wrong?  How should I measure dihedral restraint over
time?

Thanks.

Sadaf
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Re: [gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy"

[Justin Lemkul]

On 2/26/20 8:10 PM, Anh Mai wrote:

Hi all,
Could someone please help me?

I have a question about the *temperature outputs *from the two
packages "gmx traj"
and "gmx energy."

I used the two packages to export the Temperature of a "Protein" group.
Here is what I did.

1. gmx traj -f trajectory_with_velocity.trr -s topology.tpr -ot
Temperature_traj.xvg
gmx analyze -f Temperature_traj.xvg
*Found: Temperature_traj = 250.475 K*
2. gmx energy -f energy.edr
Select "14 Temperature".
*Found: Temperature_energy = 300.137 K*

Our *parameters.mdp* file has:
"...
constraints =  h-bonds
constraint_algorithm = Lincs

tc-grps=  System ; sd integrator (!)
tau_t   =  2.0 ; sd integrator (!)
ref_t   =  300

gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
..."

I don't know why the two temperatures are that much different from each
other, such as by 50 degrees.
Looking forward to an explanation.


gmx traj knows nothing about constraints so the number of degrees of 
freedom for the calculation are incorrect.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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[gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy"

[Anh Mai]

Hi all,
Could someone please help me?

I have a question about the *temperature outputs *from the two
packages "gmx traj"
and "gmx energy."

I used the two packages to export the Temperature of a "Protein" group.
Here is what I did.

   1. gmx traj -f trajectory_with_velocity.trr -s topology.tpr -ot
   Temperature_traj.xvg
   gmx analyze -f Temperature_traj.xvg
   *Found: Temperature_traj = 250.475 K*
   2. gmx energy -f energy.edr
   Select "14 Temperature".
   *Found: Temperature_energy = 300.137 K*

Our *parameters.mdp* file has:
"...
constraints =  h-bonds
constraint_algorithm = Lincs

tc-grps=  System ; sd integrator (!)
tau_t   =  2.0 ; sd integrator (!)
ref_t   =  300

gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
..."

I don't know why the two temperatures are that much different from each
other, such as by 50 degrees.
Looking forward to an explanation.
Thanks a lot.

Sincerely yours,
Anh Mai
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Re: [gmx-users] Fwd: error during ions.tpr genereation.

[Justin Lemkul]

On 2/26/20 1:26 PM, Neha Tiwari wrote:

Dear all,
I want to know if there is any error in the .itp file of ligand attached


The mailing list does not accept attachments.


here, the ligand molecule was refined and optimized using G03 calculation
and .itp was generated using the ATB server.
As I am unable to generate any extension files in GROMACS using this.



If you are getting a specific error, please quote it directly (copy and 
paste from your terminal) and provide it to us. In the absence of an 
actual error, there's nothing anyone can do to help you.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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[gmx-users] Fwd: error during ions.tpr genereation.

[Neha Tiwari]

Dear all,
I want to know if there is any error in the .itp file of ligand attached
here, the ligand molecule was refined and optimized using G03 calculation
and .itp was generated using the ATB server.
As I am unable to generate any extension files in GROMACS using this.


Please help.
Neha.
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[gmx-users] Fwd: restraints failure problem

[Sadaf Rani]

Dear Gromacs users

I am posting this problem third time in hope to get some suggestions
regarding my problem.
I am doing a test calculation in MD simulation between ligand and a protein
residue for bond angle and dihedral restraints. I have set them in my
topology file as below:-
; distance restraints
[ bonds ]
;ij type r0A r1A r2AfcAr0B r1B
r2BfcB
712910 0.403   0.403   10.0   0.00.403   0.403   10.0
4184.000

[ angle_restraints ]
;   aiajakal  typethA  fcAmultA  thB  fcB
 multB
29716971   1  104.92   0.01 104.92   41.840   1
71293129   1  147.02   0.01 147.02   41.840   1

[ dihedral_restraints ]
;   aiajakal   typephiA dphiA  fcAphiB  dphiB
 fcB
69712931   1146.72 0.00.0   146.72 0.0
41.840
7271 2931   1 17.55  0.00.017.55 0.0
41.840
7271 2925   1 173.10 0.00.0   173.10 0.0
41.840

However, after energy minimization, I observed that my restraints are not
working and I find the following change:-

bonds changed from 0.403 *0.401*
angles:-
104.92   changed to *107.98*
147.02  changed to *152.76*
dihedrals:-
 146.72  changed to *141.72*
 17.55  changed to 2*2.13*
173.10  changed to *174.23*
  The fluctuation in restraints goes on increasing till the production run
which shows that my restraints are not working.
How should I work with these so that they may not change much? Do I need to
increase force for restraints if yes then how much increase? any idea?  I
have tried these simulations with position restraints. Is the method of
putting restraints correct or should I try some other? I have to apply
these in the free energy calculation which already crashed because of
restraint failure.
I would really be thankful for your kind suggestions, please.

Thanks.
Sadaf
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[gmx-users] Fwd: Which output of gmx energy represents stress

[Pragati Sharma]

Dear all,

I am calculating stress-strain using uniaxial deformation with deform
option. Which output of gmx energy represents stress

*Is it Press-XX or VIR-XX,* or some other value.(supposing the deformation
is in x direction)

Thanks in advance,
Pragati
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Re: [gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU

[Szilárd Páll]

Hi Oliver,

Does this affect an installation of GROMACS? In previous reports we have
observed that the issue is only present when running "make check" in the
build tree, but not in the case of an installed version.

Cheers,
--
Szilárd


On Mon, Feb 17, 2020 at 7:58 PM Oliver Dutton  wrote:

> Hello,
>
> I am trying to do the exact same as Michael in
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html
> <
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html
> >
>  but hit the exact same error of it not finding a simple header file. I’ve
> tried building 2019.5 and 2020 Gromacs on a MacBook Pro with AMD Radeon Pro
> 560 GPU.
>
> I’m using the apple inbuilt compiler, same flags and cmake options as
> Michael. Was this ever got working?
>
> Kind regards,
> Oliver
>
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[gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU

[Oliver Dutton]

Hello,

I am trying to do the exact same as Michael in 
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html
 

 but hit the exact same error of it not finding a simple header file. I’ve 
tried building 2019.5 and 2020 Gromacs on a MacBook Pro with AMD Radeon Pro 560 
GPU. 

I’m using the apple inbuilt compiler, same flags and cmake options as Michael. 
Was this ever got working?

Kind regards,
Oliver

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Re: [gmx-users] Fwd:

[Alessandra Villa]

HI,
Are you using a third-party tools for MMPBSA analysis?
You could ask directly to the authors
Best regards
Alessandra


On Wed, Feb 5, 2020 at 7:19 AM saranya  wrote:

> I have performed a simulation for a protein-metal cluster complex system
> for 500ns. While calculating MMPBSA analysis for the system, I had
> selected
> two ranges of Trajectory period (100-110 ns; 290-300 ns) based on RMSD
> profile of protein-metal cluster 500 ns simulation period and executed the
> commands for a single range of trajectory period. In the result of the
> binding energy of my system, values are void. Hence, I Kindly need your
> valuable suggestions in this regard. Herewith I have attached the obtained
> results of my system,
>
>
> #Complex Number:1
> ===
>SUMMARY
> ===
>
>
>  van der Waal energy  =   -1144.250   +/-   28.405 kJ/mol
>
>  Electrostattic energy=   0.000   +/-0.000 kJ/mol
>
>  Polar solvation energy   = nan   +/-  nan kJ/mol
>
>  SASA energy  = -25.841   +/-1.107 kJ/mol
>
>  SAV energy   =   0.000   +/-0.000 kJ/mol
>
>  WCA energy   =   0.000   +/-0.000 kJ/mol
>
>  Binding energy   = nan   +/-  nan kJ/mol
>
> ===
> END
> ===
>
>
>
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
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[gmx-users] Fwd:

[saranya]

I have performed a simulation for a protein-metal cluster complex system
for 500ns. While calculating MMPBSA analysis for the system, I had selected
two ranges of Trajectory period (100-110 ns; 290-300 ns) based on RMSD
profile of protein-metal cluster 500 ns simulation period and executed the
commands for a single range of trajectory period. In the result of the
binding energy of my system, values are void. Hence, I Kindly need your
valuable suggestions in this regard. Herewith I have attached the obtained
results of my system,


#Complex Number:1
===
   SUMMARY
===


 van der Waal energy  =   -1144.250   +/-   28.405 kJ/mol

 Electrostattic energy=   0.000   +/-0.000 kJ/mol

 Polar solvation energy   = nan   +/-  nan kJ/mol

 SASA energy  = -25.841   +/-1.107 kJ/mol

 SAV energy   =   0.000   +/-0.000 kJ/mol

 WCA energy   =   0.000   +/-0.000 kJ/mol

 Binding energy   = nan   +/-  nan kJ/mol

===
END
===




*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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[gmx-users] Fwd:

[Sadaf Rani]

Energy minimization getting jumps

Dear Gromacs users
I am running a free energy calculation of the protein-ligand complex.
During the energy minimization process, I am getting many jumps in steps as
below:-

Step   Time
  1050010500.0

   Energies (kJ/mol)
   Bond Restraint Pot.  AngleProper Dih.  Improper Dih.
1.20860e+031.65864e+004.67218e+031.83350e+041.87873e+02
  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
6.81295e+037.12692e+043.37954e+05   -6.56537e+03   -2.70668e+06
   Coul. recip.Angle Rest. Dih. Rest.  Potential Pres. DC (bar)
4.78029e+035.32468e+003.32764e+00   -2.26802e+060.0e+00
 Pressure (bar)dVremain/dl   dEkin/dl  dVcoul/dl   dVvdw/dl
   -2.69428e+040.0e+000.0e+002.78529e+03   -1.65404e+02
 dVrestraint/dl   Constr. rmsd
0.0e+002.71623e-06

   Step   Time
  1050110501.0

   Step   Time
  1050210502.0

   Step   Time
  1050310503.0

   Step   Time
  1050410504.0

   Step   Time
  1050510505.0

   Step   Time
  1050610506.0

   Step   Time
  1050710507.0

   Step   Time
  1050810508.0

   Step   Time
  1050910509.0

   Step   Time
  1051010510.0

   Step   Time
  1051110511.0


Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (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 10512 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -2.2680185e+06
Maximum force =  6.3521606e+02 on atom 4653
Norm of force =  3.6713926e+00

Should I use double precision for energy minimization?
I need your suggestions,
 please.

Thanks

Sadaf Rani
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[gmx-users] Fwd: A list of missing interactions

[Sadaf Rani]

Dear Gromacs users
I am facing this error during free energy calculation of protein-ligand for
which I have applied restrained to some atoms of protein residue and
ligand.
A list of missing interactions:
  Restraint Pot. of  1 missing  1

Molecule type 'Protein'
the first 10 missing interactions, except for exclusions:
  Restraint Pot. atoms 3437 7908   global  3437  7908

---
Program: gmx mdrun, version 2018.1
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:0 (out of 2)

Fatal error:
1 of the 64584 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance (4.47682
nm)
or the two-body cut-off distance (4.47682 nm), see option -rdd, for pairs
and
tabulated bonds also see option -ddcheck

Could anybody please suggest how should I fix this error? I would be really
thankful.

Regards

Sadaf
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Re: [gmx-users] Fwd: setting ionic liquid simulation in gromacs

[Bratin Kumar Das]

Hi
What error you are getting?

On Fri 20 Dec, 2019, 1:14 PM Devargya Chakraborty, <
devargyachakraborty@gmail.com> wrote:

> -- Forwarded message -
> From: Devargya Chakraborty 
> Date: Thu, 19 Dec 2019 at 18:17
> Subject: setting ionic liquid simulation in gromacs
> To: 
>
>
> can any body guide me or tell me the steps for the simulation of ionic
> liquid and how to properly use the .itp files available for the cations and
> anions. i am getting error while setting the force-field of the ionic
> liquid. any help regarding the topic will be welcomed.
> --
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[gmx-users] Fwd: setting ionic liquid simulation in gromacs

[Devargya Chakraborty]

-- Forwarded message -
From: Devargya Chakraborty 
Date: Thu, 19 Dec 2019 at 18:17
Subject: setting ionic liquid simulation in gromacs
To: 


can any body guide me or tell me the steps for the simulation of ionic
liquid and how to properly use the .itp files available for the cations and
anions. i am getting error while setting the force-field of the ionic
liquid. any help regarding the topic will be welcomed.
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[gmx-users] Fwd: solvent evaporation modeling

[SAKO MIRZAIE]

Dear André,

Thank you for your response.
Could you send me such a script?

Best
--
***
Sako

On Mon, Dec 2, 2019 at 12:54 AM SAKO MIRZAIE  wrote:

> Dear André,
>
> Thank you for your response.
> Could you send me such a script?
>
> On Sun, Dec 1, 2019 at 7:15 PM André Farias de Moura 
> wrote:
>
>> Dear Sako,
>>
>> we did something like that a few years ago, please take a look at DOI 
>> 10.1039/C4CP03519D
>> for details.
>>
>> in a nutshell: you need a script that runs a sequence of short
>> equilibration and production runs after a number of solvent molecules are
>> removed (implying that topology needs to be updated for the number of
>> solvent molecules at each round, so the script needs to include some
>> parsing of the files as well).
>>
>> Andre
>>
>> On Sun, Dec 1, 2019 at 8:03 PM SAKO MIRZAIE 
>> wrote:
>>
>>> Hi All,
>>>
>>> I want to simulate a polymer: protein system in a way that water solvent
>>> will evaporated gradually. How should I do that? What parameters are
>>> needed
>>> to be included in the mdp file.
>>>
>>> Best
>>>
>>>
>>>
>>> --
>>> ***
>>> Sako
>>> --
>>> 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.
>>>
>>
>>
>> --
>> _
>>
>> Prof. Dr. André Farias de Moura
>> Department of Chemistry
>> Federal University of São Carlos
>> São Carlos - Brazil
>> phone: +55-16-3351-8090
>>
>
>
> --
> ***
> Sako
>
>
>
>
>
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Re: [gmx-users] Fwd: gmx trjcat

[Elton Carvalho]

Hello,

The advantage of text based trajectory files is that they are... text
based, which means that usual tools for treating text files, such as cat
and sed, can be used to treat text-based trajectories.

Concatenating .gro or .pdb files can be accomplished literally
concatenating the files: in POSIX-like systems (linux, macos and
recent enough versions of win10 (with some abuse of definitions)) a
command like 'cat *.gro > traj.gro'. If there are timestamps on the frames
(e.g. t=XXX in gro files), you may need to do some editing.

Cheers,
Elton

On Mon, Oct 28, 2019 at 12:18 PM Paul bauer  wrote:

> Hello,
>
> I think I understood your problem (or at least hope so).
> The issue is that it is no longer possible to directly concatenate text
> based trajectory files, so I showed a possible way to work around the
> problem.
> You can also go back to a previous version of GROMACS to perform the
> concatenation, but I can't promise you that it will work.
>
> Please let me know if you need extra help to get this to work.
>
> @Justin, here is the change that added the check for binary file
> formats: c232242c29fb3ca63c8e1027eb70477069decdd9
>
> Cheers
>
> Paul
>
> On 28/10/2019 15:42, Alex wrote:
> > Hi,
> > Paul,
> > I guess you understood the question wrongly. I have some *.gro files and
> I
> > want to concatenate them to have a trr (or xtc) trajectory.
> >
> > Justin,
> > Yes indeed, It would be great if gmx trjcat could concatenate the gro
> files.
> >
> > Regards,
> > Alex
> >
> > On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul  wrote:
> >
> >>
> >> On 10/28/19 6:26 AM, Paul bauer wrote:
> >>> Hello,
> >>>
> >>> this looks like a case of misleading documentation. Can you file an
> >>> issue for this please on redmine.gromacs.org?
> >>> So that we don't forgot to fix this for the next patch release?
> >>> A possible work around for you can be that you first convert your
> >>> files to e.g. XTC format, use trjcat to combine them and convert them
> >>> back to GRO.
> >>>
> >> Out of curiosity, why was this file format removed as an input for
> >> trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB
> >> files to make a psuedo-trajectory for ensemble analysis was rather
> >> handy. Converting to an intermediate binary format is a workaround, but
> >> why add the extra step? Did the trjcat code need de-complicating?
> >>
> >> -Justin
> >>
> >>> Cheers
> >>>
> >>> Paul
> >>>
> >>>
> >>> On 27/10/2019 19:47, Alex wrote:
>  Any comment on this, please?
>  Thanks
>  -- Forwarded message -
>  From: Alex 
>  Date: Sat, Oct 26, 2019 at 9:38 AM
>  Subject: gmx trjcat
>  To: 
> 
> 
>  Dear all,
>  I want to concatenate some gro file to have a trr or xtc trajectory
> file
>  out of them as gro files are also acceptable as input files,
>  according the
>  gmx trjcat man page;
> 
>  Options to specify input files:
> -f  [<.xtc/.trr/...> [...]] (traj.xtc)
>   Trajectory: xtc trr cpt *gro* g96 pdb tng
> 
>  So, I fed the .gro files in as input files likes;
>  gmx trjcat -f c*.gro -o trajout.trr
> 
>  However, I get below error that;
>  Fatal error:
>  gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)
> 
>  Any comment is highly appreciated.
>  Regards,
>  Alex
> >>>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> 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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> >>
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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.
>
>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
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-- 
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Re: [gmx-users] Fwd: gmx trjcat

[Alex]

Hi Paul,

I though you mean converting the .gro files to .xtc file using *trjcat *(which
was my initial question), sorry about that.
I see now, I just used *trjconv* to convert gro file them to .xtc files and
then ... .

.gro trjconv> .xtc --trjcat> .xtc(or trr)

Thanks
Alex

On Mon, Oct 28, 2019 at 11:18 AM Paul bauer  wrote:

> Hello,
>
> I think I understood your problem (or at least hope so).
> The issue is that it is no longer possible to directly concatenate text
> based trajectory files, so I showed a possible way to work around the
> problem.
> You can also go back to a previous version of GROMACS to perform the
> concatenation, but I can't promise you that it will work.
>
> Please let me know if you need extra help to get this to work.
>
> @Justin, here is the change that added the check for binary file
> formats: c232242c29fb3ca63c8e1027eb70477069decdd9
>
> Cheers
>
> Paul
>
> On 28/10/2019 15:42, Alex wrote:
> > Hi,
> > Paul,
> > I guess you understood the question wrongly. I have some *.gro files and
> I
> > want to concatenate them to have a trr (or xtc) trajectory.
> >
> > Justin,
> > Yes indeed, It would be great if gmx trjcat could concatenate the gro
> files.
> >
> > Regards,
> > Alex
> >
> > On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul  wrote:
> >
> >>
> >> On 10/28/19 6:26 AM, Paul bauer wrote:
> >>> Hello,
> >>>
> >>> this looks like a case of misleading documentation. Can you file an
> >>> issue for this please on redmine.gromacs.org?
> >>> So that we don't forgot to fix this for the next patch release?
> >>> A possible work around for you can be that you first convert your
> >>> files to e.g. XTC format, use trjcat to combine them and convert them
> >>> back to GRO.
> >>>
> >> Out of curiosity, why was this file format removed as an input for
> >> trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB
> >> files to make a psuedo-trajectory for ensemble analysis was rather
> >> handy. Converting to an intermediate binary format is a workaround, but
> >> why add the extra step? Did the trjcat code need de-complicating?
> >>
> >> -Justin
> >>
> >>> Cheers
> >>>
> >>> Paul
> >>>
> >>>
> >>> On 27/10/2019 19:47, Alex wrote:
>  Any comment on this, please?
>  Thanks
>  -- Forwarded message -
>  From: Alex 
>  Date: Sat, Oct 26, 2019 at 9:38 AM
>  Subject: gmx trjcat
>  To: 
> 
> 
>  Dear all,
>  I want to concatenate some gro file to have a trr or xtc trajectory
> file
>  out of them as gro files are also acceptable as input files,
>  according the
>  gmx trjcat man page;
> 
>  Options to specify input files:
> -f  [<.xtc/.trr/...> [...]] (traj.xtc)
>   Trajectory: xtc trr cpt *gro* g96 pdb tng
> 
>  So, I fed the .gro files in as input files likes;
>  gmx trjcat -f c*.gro -o trajout.trr
> 
>  However, I get below error that;
>  Fatal error:
>  gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)
> 
>  Any comment is highly appreciated.
>  Regards,
>  Alex
> >>>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.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
> >>
> >> * 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.
>
>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
> --
> 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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>
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Re: [gmx-users] Fwd: gmx trjcat

[Paul bauer]

Hello,

I think I understood your problem (or at least hope so).
The issue is that it is no longer possible to directly concatenate text 
based trajectory files, so I showed a possible way to work around the 
problem.
You can also go back to a previous version of GROMACS to perform the 
concatenation, but I can't promise you that it will work.


Please let me know if you need extra help to get this to work.

@Justin, here is the change that added the check for binary file 
formats: c232242c29fb3ca63c8e1027eb70477069decdd9


Cheers

Paul

On 28/10/2019 15:42, Alex wrote:

Hi,
Paul,
I guess you understood the question wrongly. I have some *.gro files and I
want to concatenate them to have a trr (or xtc) trajectory.

Justin,
Yes indeed, It would be great if gmx trjcat could concatenate the gro files.

Regards,
Alex

On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul  wrote:



On 10/28/19 6:26 AM, Paul bauer wrote:

Hello,

this looks like a case of misleading documentation. Can you file an
issue for this please on redmine.gromacs.org?
So that we don't forgot to fix this for the next patch release?
A possible work around for you can be that you first convert your
files to e.g. XTC format, use trjcat to combine them and convert them
back to GRO.


Out of curiosity, why was this file format removed as an input for
trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB
files to make a psuedo-trajectory for ensemble analysis was rather
handy. Converting to an intermediate binary format is a workaround, but
why add the extra step? Did the trjcat code need de-complicating?

-Justin


Cheers

Paul


On 27/10/2019 19:47, Alex wrote:

Any comment on this, please?
Thanks
-- Forwarded message -
From: Alex 
Date: Sat, Oct 26, 2019 at 9:38 AM
Subject: gmx trjcat
To: 


Dear all,
I want to concatenate some gro file to have a trr or xtc trajectory file
out of them as gro files are also acceptable as input files,
according the
gmx trjcat man page;

Options to specify input files:
   -f  [<.xtc/.trr/...> [...]] (traj.xtc)
 Trajectory: xtc trr cpt *gro* g96 pdb tng

So, I fed the .gro files in as input files likes;
gmx trjcat -f c*.gro -o trajout.trr

However, I get below error that;
Fatal error:
gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)

Any comment is highly appreciated.
Regards,
Alex



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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--
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GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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Re: [gmx-users] Fwd: gmx trjcat

[Justin Lemkul]

On 10/28/19 10:42 AM, Alex wrote:

Hi,
Paul,
I guess you understood the question wrongly. I have some *.gro files and I
want to concatenate them to have a trr (or xtc) trajectory.


I don't think Paul misunderstood at all. The version of trjcat that 
you're using does not support an operation it once did - to concatenate 
coordinate files. You have to do an extra step, converting each .gro to 
an .xtc frame, before invoking trjcat. His solution gets around your 
problem.


-Justin


Justin,
Yes indeed, It would be great if gmx trjcat could concatenate the gro files.

Regards,
Alex

On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul  wrote:



On 10/28/19 6:26 AM, Paul bauer wrote:

Hello,

this looks like a case of misleading documentation. Can you file an
issue for this please on redmine.gromacs.org?
So that we don't forgot to fix this for the next patch release?
A possible work around for you can be that you first convert your
files to e.g. XTC format, use trjcat to combine them and convert them
back to GRO.


Out of curiosity, why was this file format removed as an input for
trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB
files to make a psuedo-trajectory for ensemble analysis was rather
handy. Converting to an intermediate binary format is a workaround, but
why add the extra step? Did the trjcat code need de-complicating?

-Justin


Cheers

Paul


On 27/10/2019 19:47, Alex wrote:

Any comment on this, please?
Thanks
-- Forwarded message -
From: Alex 
Date: Sat, Oct 26, 2019 at 9:38 AM
Subject: gmx trjcat
To: 


Dear all,
I want to concatenate some gro file to have a trr or xtc trajectory file
out of them as gro files are also acceptable as input files,
according the
gmx trjcat man page;

Options to specify input files:
   -f  [<.xtc/.trr/...> [...]] (traj.xtc)
 Trajectory: xtc trr cpt *gro* g96 pdb tng

So, I fed the .gro files in as input files likes;
gmx trjcat -f c*.gro -o trajout.trr

However, I get below error that;
Fatal error:
gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)

Any comment is highly appreciated.
Regards,
Alex



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

--
Gromacs Users mailing list

* Please search the archive at
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send a mail to gmx-users-requ...@gromacs.org.


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Re: [gmx-users] Fwd: gmx trjcat

[Alex]

Hi,
Paul,
I guess you understood the question wrongly. I have some *.gro files and I
want to concatenate them to have a trr (or xtc) trajectory.

Justin,
Yes indeed, It would be great if gmx trjcat could concatenate the gro files.

Regards,
Alex

On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul  wrote:

>
>
> On 10/28/19 6:26 AM, Paul bauer wrote:
> > Hello,
> >
> > this looks like a case of misleading documentation. Can you file an
> > issue for this please on redmine.gromacs.org?
> > So that we don't forgot to fix this for the next patch release?
> > A possible work around for you can be that you first convert your
> > files to e.g. XTC format, use trjcat to combine them and convert them
> > back to GRO.
> >
>
> Out of curiosity, why was this file format removed as an input for
> trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB
> files to make a psuedo-trajectory for ensemble analysis was rather
> handy. Converting to an intermediate binary format is a workaround, but
> why add the extra step? Did the trjcat code need de-complicating?
>
> -Justin
>
> > Cheers
> >
> > Paul
> >
> >
> > On 27/10/2019 19:47, Alex wrote:
> >> Any comment on this, please?
> >> Thanks
> >> -- Forwarded message -
> >> From: Alex 
> >> Date: Sat, Oct 26, 2019 at 9:38 AM
> >> Subject: gmx trjcat
> >> To: 
> >>
> >>
> >> Dear all,
> >> I want to concatenate some gro file to have a trr or xtc trajectory file
> >> out of them as gro files are also acceptable as input files,
> >> according the
> >> gmx trjcat man page;
> >>
> >> Options to specify input files:
> >>   -f  [<.xtc/.trr/...> [...]] (traj.xtc)
> >> Trajectory: xtc trr cpt *gro* g96 pdb tng
> >>
> >> So, I fed the .gro files in as input files likes;
> >> gmx trjcat -f c*.gro -o trajout.trr
> >>
> >> However, I get below error that;
> >> Fatal error:
> >> gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)
> >>
> >> Any comment is highly appreciated.
> >> Regards,
> >> Alex
> >
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.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
>
> * 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] Fwd: gmx trjcat

[Justin Lemkul]

On 10/28/19 6:26 AM, Paul bauer wrote:

Hello,

this looks like a case of misleading documentation. Can you file an 
issue for this please on redmine.gromacs.org?

So that we don't forgot to fix this for the next patch release?
A possible work around for you can be that you first convert your 
files to e.g. XTC format, use trjcat to combine them and convert them 
back to GRO.




Out of curiosity, why was this file format removed as an input for 
trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB 
files to make a psuedo-trajectory for ensemble analysis was rather 
handy. Converting to an intermediate binary format is a workaround, but 
why add the extra step? Did the trjcat code need de-complicating?


-Justin


Cheers

Paul


On 27/10/2019 19:47, Alex wrote:

Any comment on this, please?
Thanks
-- Forwarded message -
From: Alex 
Date: Sat, Oct 26, 2019 at 9:38 AM
Subject: gmx trjcat
To: 


Dear all,
I want to concatenate some gro file to have a trr or xtc trajectory file
out of them as gro files are also acceptable as input files, 
according the

gmx trjcat man page;

Options to specify input files:
  -f  [<.xtc/.trr/...> [...]] (traj.xtc)
    Trajectory: xtc trr cpt *gro* g96 pdb tng

So, I fed the .gro files in as input files likes;
gmx trjcat -f c*.gro -o trajout.trr

However, I get below error that;
Fatal error:
gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)

Any comment is highly appreciated.
Regards,
Alex





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

--
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Fwd: gmx trjcat

[Paul bauer]

Hello,

this looks like a case of misleading documentation. Can you file an 
issue for this please on redmine.gromacs.org?

So that we don't forgot to fix this for the next patch release?
A possible work around for you can be that you first convert your files 
to e.g. XTC format, use trjcat to combine them and convert them back to GRO.


Cheers

Paul


On 27/10/2019 19:47, Alex wrote:

Any comment on this, please?
Thanks
-- Forwarded message -
From: Alex 
Date: Sat, Oct 26, 2019 at 9:38 AM
Subject: gmx trjcat
To: 


Dear all,
I want to concatenate some gro file to have a trr or xtc trajectory file
out of them as gro files are also acceptable as input files, according the
gmx trjcat man page;

Options to specify input files:
  -f  [<.xtc/.trr/...> [...]] (traj.xtc)
Trajectory: xtc trr cpt *gro* g96 pdb tng

So, I fed the .gro files in as input files likes;
gmx trjcat -f c*.gro -o trajout.trr

However, I get below error that;
Fatal error:
gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)

Any comment is highly appreciated.
Regards,
Alex



--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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

[gmx-users] Fwd: gmx trjcat

[Alex]

Any comment on this, please?
Thanks
-- Forwarded message -
From: Alex 
Date: Sat, Oct 26, 2019 at 9:38 AM
Subject: gmx trjcat
To: 


Dear all,
I want to concatenate some gro file to have a trr or xtc trajectory file
out of them as gro files are also acceptable as input files, according the
gmx trjcat man page;

Options to specify input files:
 -f  [<.xtc/.trr/...> [...]] (traj.xtc)
   Trajectory: xtc trr cpt *gro* g96 pdb tng

So, I fed the .gro files in as input files likes;
gmx trjcat -f c*.gro -o trajout.trr

However, I get below error that;
Fatal error:
gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)

Any comment is highly appreciated.
Regards,
Alex
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Re: [gmx-users] Fwd:

[Justin Lemkul]

On 10/27/19 6:25 AM, saranya wrote:

Hi users,
  I am performing a simulation for a protein-metal cluster complex
system. I am trying to generate itp file for the metal cluster (Au) having
144 atoms. I have taken itp file of the metal cluster (Au) with ligand from
an article(doi: 10.1016/j.colsurfa.2016.05.038) and extracted the
parameters of metal clusters alone and I used it for my system preparation.
During the energy minimization, Gromacs has shown errors like

  An input file contains a line longer than 4095 characters, while the
buffer passed to fgets2 has size 4095. The line starts with: '
'...
Kindly need your valuable suggestions in this regard.


Some file you have created is misformatted, likely due to a copy-paste 
error or use of either a non-plain-text editor or Windows-style line 
endings.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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

[gmx-users] Fwd:

[saranya]

Hi users,
 I am performing a simulation for a protein-metal cluster complex
system. I am trying to generate itp file for the metal cluster (Au) having
144 atoms. I have taken itp file of the metal cluster (Au) with ligand from
an article(doi: 10.1016/j.colsurfa.2016.05.038) and extracted the
parameters of metal clusters alone and I used it for my system preparation.
During the energy minimization, Gromacs has shown errors like

 An input file contains a line longer than 4095 characters, while the
buffer passed to fgets2 has size 4095. The line starts with: '
   '...
Kindly need your valuable suggestions in this regard.

With regards,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
-- 

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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[gmx-users] Fwd: cut in gmx clustsize

[Alex]

Any comments, please?

Thanks,
Alex

-- Forwarded message -
From: Alex 
Date: Fri, Oct 4, 2019 at 13:58
Subject: cut in gmx clustsize
To: 


Dear all,
In clustering what is usually defined as a criteria is a cut-off so that if
two atoms or molecules are closer to each other less than the cut-off then
those two are being counted to be in a cluster, I see even that in the
source code of gmx clustsize where
...
/* If distance less than cut-off */
if (bSame)
{
/* Merge clusters: check for all atoms whether they are in
* cluster cj and if so, put them in ci
*/
for (k = 0; (k < nindex); k++)
...
However, what is puzzling me is the definition of the -cut as "Largest
distance (nm) to be considered in a cluster" in gmx clustsize man page.
So, would you please elaborate that further?

Also, how the default cut-off of 0.35 nm has been indicated?

And finally, in the case of using -mol option to consider the molecules
rather than atoms in clustering, I wonder if the cut-off is the distance
between center of mass of the molecule?

Regards,
Alex
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[gmx-users] Fwd: ion flux counter

[Harutyun Sahakyan]

Dear Gromacs users,

Computational electrophysiology protocol has some analyzing tools allowing
to count ion flux etc. I have used an external electric field to simulate
the process of ion permissions through a membrane channel. How can I count
ion flux, conductivity or something like that?

Best wishes,
Harutyun Sahakyan
Senior Assistant at Laboratory of
Computational Modeling of Biological Processes,
Institute of Molecular Biology, NAS, Armenia, Yerevan
Tel: +374 93 323990
h_sahak...@mb.sci.am
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Re: [gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

Hi Mark,
thank you for your reply. I inspected CMakeError.log and CMakeOutputlog:
though several errors were reported in the first one, no mention to
GmxDetectCpu at all.
When trying "cmake --debug-trycompile $builddir -UCPU_DETECTION_COMPILED",
the output is:
"debug trycompile on
-- The GROMACS-managed build of FFTW 3 will configure with the following
optimizations:
-- Configuring done
-- Generating done
-- Build files have been written to: /home/stefano/gromacs-2019.2/build"
and $builddir/CMakeFiles/CMakeTmp directory contains some files and
subdirectories but, to be honest, I have no idea where to find possibly
relevant information.
CMakeError.log and CMakeOutputlog files can be found at:
https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0

Stefano

Il giorno gio 12 set 2019 alle ore 18:16 Mark Abraham <
mark.j.abra...@gmail.com> ha scritto:

> Hi,
>
> In that case, I would look at
>
> $builddir/CMakeFiles/CMakeError.log (and maybe
> $builddir/CMakeFiles/CMakeOutput.log)
>
> to see what was reported about that attempted compilation of GmxDetectCpu
> program. Depending what is learned, you might want to try your usual cmake
> call, and then
>
> cmake --debug-trycompile $builddir -UCPU_DETECTION_COMPILED
>
> and the contents of $builddir/CMakeFiles/CMakeTmp directory might also help
>
> (docs at https://cmake.org/cmake/help/latest/command/try_compile.html)
>
> Mark
>
> On Thu, 12 Sep 2019 at 17:52, Stefano Guglielmo <
> stefano.guglie...@unito.it>
> wrote:
>
> > Hi Mark,
> > actually running cmake in the output I can read "Did not detect build CPU
> > vendor - detection program did not compile".
> > Any suggestions about the origin of the issue and possible solutions?
> >
> > Thanks
> > Stefano
> >
> > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > Mail
> > priva di virus. www.avast.com
> > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >
> > Il giorno gio 12 set 2019 alle ore 17:26 Mark Abraham <
> > mark.j.abra...@gmail.com> ha scritto:
> >
> > > Hi,
> > >
> > > There will have been reports by cmake about whether the detection
> program
> > > compiled and/or ran successfully, which would be useful diagnostic
> > > information. Please run cmake in a fresh build directory and look for
> > that.
> > > It is possible to run that program individually, if the issue is that
> it
> > > compiles and fails to run somehow (e.g. that linking is broken)
> > >
> > > Mark
> > >
> > > On Thu, 12 Sep 2019 at 17:06, Stefano Guglielmo <
> > > stefano.guglie...@unito.it>
> > > wrote:
> > >
> > > > I cannot say about BIOS/firmware yet, I made a quite "standard"
> > > > installation of centOS 7, but I'll try to check; as for cpu, for what
> > it
> > > > means, I made the stress test which brought up temperature for two
> > hours
> > > > together with gpu_burn, so I would exclude cooling failure.
> > > >
> > > > A further update: I yum-installed devtoolset-8-toolchain, so now
> cmake
> > > > finds gcc 8.3.1, but again SIMD instructions detection failed.
> > > > Sorry for bothering but I must say that I am getting a bit confused.
> > > >
> > > > Stefano
> > > >
> > > > <
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > > >
> > > > Mail
> > > > priva di virus. www.avast.com
> > > > <
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > > >
> > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > >
> > > > Il giorno gio 12 set 2019 alle ore 16:35 Szilárd Páll <
> > > > pall.szil...@gmail.com> ha scritto:
> > > >
> > > > > On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo
> > > > >  wrote:
> > > > > >
> > > > > > As an update, I have just tried a run with cpu only after
> compiling
> > > > with
> > > > > > AVX2_128 and the workstation turned off after few minutes.
> > > > >
> > > > > That is suspicious. Perhaps a CPU cooling issue? Otherwise you may
> > > > > have a BIOS/firmware issue or, less likely but possibly, a a faulty
> > > > > CPU.
> > > > >
> > > > > --
> > > > > Szilárd
> > > > >
> > > > > > <
> > > > >
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > > > >
> > > > > > Mail
> > > > > > priva di virus. www.avast.com
> > > > > > <
> > > > >
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > > > >
> > > > > > <#m_360888458910571867_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > > > >
> > > > > > Il giorno gio 12 set 2019 alle ore 15:19 Stefano Guglielmo <
> > > > > > stefano.guglie...@unito.it> ha scritto:
> > > > > >
> > > > > > > Hi Szilard,
> > > > > > > thanks for your reply.
> > > > > > > The compiler is gcc 4.8.5.
> > > > > > > I put below the 

Re: [gmx-users] Fwd: SIMD options

[Mark Abraham]

Hi,

In that case, I would look at

$builddir/CMakeFiles/CMakeError.log (and maybe
$builddir/CMakeFiles/CMakeOutput.log)

to see what was reported about that attempted compilation of GmxDetectCpu
program. Depending what is learned, you might want to try your usual cmake
call, and then

cmake --debug-trycompile $builddir -UCPU_DETECTION_COMPILED

and the contents of $builddir/CMakeFiles/CMakeTmp directory might also help

(docs at https://cmake.org/cmake/help/latest/command/try_compile.html)

Mark

On Thu, 12 Sep 2019 at 17:52, Stefano Guglielmo 
wrote:

> Hi Mark,
> actually running cmake in the output I can read "Did not detect build CPU
> vendor - detection program did not compile".
> Any suggestions about the origin of the issue and possible solutions?
>
> Thanks
> Stefano
>
> <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> Mail
> priva di virus. www.avast.com
> <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> Il giorno gio 12 set 2019 alle ore 17:26 Mark Abraham <
> mark.j.abra...@gmail.com> ha scritto:
>
> > Hi,
> >
> > There will have been reports by cmake about whether the detection program
> > compiled and/or ran successfully, which would be useful diagnostic
> > information. Please run cmake in a fresh build directory and look for
> that.
> > It is possible to run that program individually, if the issue is that it
> > compiles and fails to run somehow (e.g. that linking is broken)
> >
> > Mark
> >
> > On Thu, 12 Sep 2019 at 17:06, Stefano Guglielmo <
> > stefano.guglie...@unito.it>
> > wrote:
> >
> > > I cannot say about BIOS/firmware yet, I made a quite "standard"
> > > installation of centOS 7, but I'll try to check; as for cpu, for what
> it
> > > means, I made the stress test which brought up temperature for two
> hours
> > > together with gpu_burn, so I would exclude cooling failure.
> > >
> > > A further update: I yum-installed devtoolset-8-toolchain, so now cmake
> > > finds gcc 8.3.1, but again SIMD instructions detection failed.
> > > Sorry for bothering but I must say that I am getting a bit confused.
> > >
> > > Stefano
> > >
> > > <
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > >
> > > Mail
> > > priva di virus. www.avast.com
> > > <
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > >
> > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > >
> > > Il giorno gio 12 set 2019 alle ore 16:35 Szilárd Páll <
> > > pall.szil...@gmail.com> ha scritto:
> > >
> > > > On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo
> > > >  wrote:
> > > > >
> > > > > As an update, I have just tried a run with cpu only after compiling
> > > with
> > > > > AVX2_128 and the workstation turned off after few minutes.
> > > >
> > > > That is suspicious. Perhaps a CPU cooling issue? Otherwise you may
> > > > have a BIOS/firmware issue or, less likely but possibly, a a faulty
> > > > CPU.
> > > >
> > > > --
> > > > Szilárd
> > > >
> > > > > <
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > > >
> > > > > Mail
> > > > > priva di virus. www.avast.com
> > > > > <
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > > >
> > > > > <#m_360888458910571867_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > > >
> > > > > Il giorno gio 12 set 2019 alle ore 15:19 Stefano Guglielmo <
> > > > > stefano.guglie...@unito.it> ha scritto:
> > > > >
> > > > > > Hi Szilard,
> > > > > > thanks for your reply.
> > > > > > The compiler is gcc 4.8.5.
> > > > > > I put below the link where you can find the files coming from
> cmake
> > > and
> > > > > > the output for "AUTO" SIMD instruction. As for cpu only, as you
> had
> > > > > > suggested previously I tried a run (after compiling with
> AVX2_256)
> > > and
> > > > it
> > > > > > worked without any problems for about 5 hours. I will try with
> > > > AVX2_128 as
> > > > > > well.
> > > > > >
> > > > > > Stefano
> > > > > >
> > > > > >
> > > >
> > >
> >
> https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0
> > > > > >
> > > > > >
> > > > > > <
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > >
> > > > Mail
> > > > > > priva di virus. www.avast.com
> > > > > > <
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > > >
> > > > > >
> > > >
> > >
> >
> <#m_360888458910571867_m_-3568712886600561053_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > > > >
> > > > > > Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll <
> > > > > > pall.szil...@gmail.com> ha scritto:
> > > > > >
> > > > > >> On Thu, Sep 12, 2019 at 8:58 AM 

Re: [gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

Hi Mark,
actually running cmake in the output I can read "Did not detect build CPU
vendor - detection program did not compile".
Any suggestions about the origin of the issue and possible solutions?

Thanks
Stefano


Mail
priva di virus. www.avast.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

Il giorno gio 12 set 2019 alle ore 17:26 Mark Abraham <
mark.j.abra...@gmail.com> ha scritto:

> Hi,
>
> There will have been reports by cmake about whether the detection program
> compiled and/or ran successfully, which would be useful diagnostic
> information. Please run cmake in a fresh build directory and look for that.
> It is possible to run that program individually, if the issue is that it
> compiles and fails to run somehow (e.g. that linking is broken)
>
> Mark
>
> On Thu, 12 Sep 2019 at 17:06, Stefano Guglielmo <
> stefano.guglie...@unito.it>
> wrote:
>
> > I cannot say about BIOS/firmware yet, I made a quite "standard"
> > installation of centOS 7, but I'll try to check; as for cpu, for what it
> > means, I made the stress test which brought up temperature for two hours
> > together with gpu_burn, so I would exclude cooling failure.
> >
> > A further update: I yum-installed devtoolset-8-toolchain, so now cmake
> > finds gcc 8.3.1, but again SIMD instructions detection failed.
> > Sorry for bothering but I must say that I am getting a bit confused.
> >
> > Stefano
> >
> > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > Mail
> > priva di virus. www.avast.com
> > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >
> > Il giorno gio 12 set 2019 alle ore 16:35 Szilárd Páll <
> > pall.szil...@gmail.com> ha scritto:
> >
> > > On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo
> > >  wrote:
> > > >
> > > > As an update, I have just tried a run with cpu only after compiling
> > with
> > > > AVX2_128 and the workstation turned off after few minutes.
> > >
> > > That is suspicious. Perhaps a CPU cooling issue? Otherwise you may
> > > have a BIOS/firmware issue or, less likely but possibly, a a faulty
> > > CPU.
> > >
> > > --
> > > Szilárd
> > >
> > > > <
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > >
> > > > Mail
> > > > priva di virus. www.avast.com
> > > > <
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > >
> > > > <#m_360888458910571867_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > >
> > > > Il giorno gio 12 set 2019 alle ore 15:19 Stefano Guglielmo <
> > > > stefano.guglie...@unito.it> ha scritto:
> > > >
> > > > > Hi Szilard,
> > > > > thanks for your reply.
> > > > > The compiler is gcc 4.8.5.
> > > > > I put below the link where you can find the files coming from cmake
> > and
> > > > > the output for "AUTO" SIMD instruction. As for cpu only, as you had
> > > > > suggested previously I tried a run (after compiling with AVX2_256)
> > and
> > > it
> > > > > worked without any problems for about 5 hours. I will try with
> > > AVX2_128 as
> > > > > well.
> > > > >
> > > > > Stefano
> > > > >
> > > > >
> > >
> >
> https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0
> > > > >
> > > > >
> > > > > <
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > > Mail
> > > > > priva di virus. www.avast.com
> > > > > <
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > > >
> > > > >
> > >
> >
> <#m_360888458910571867_m_-3568712886600561053_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > > >
> > > > > Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll <
> > > > > pall.szil...@gmail.com> ha scritto:
> > > > >
> > > > >> On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
> > > > >>  wrote:
> > > > >> >
> > > > >> > I apologize for the mistake, there was a typo in the object that
> > > could
> > > > >> be
> > > > >> > misleading, so I re-post with the correct object,
> > > > >> > sorry.
> > > > >> >
> > > > >> > -- Forwarded message -
> > > > >> > Da: Stefano Guglielmo 
> > > > >> > Date: mer 11 set 2019 alle ore 17:17
> > > > >> > Subject: SMD options
> > > > >> > To: 
> > > > >> >
> > > > >> >
> > > > >> > Hi all,
> > > > >> > following my previous post regarding anomalous crashing of the
> > > system on
> > > > >> > running gromacs on two gpus, I have some new elements to add.
> > > > >> > I tested the workstation with two tools for gpu and cpu I found
> on
> > > the
> > > > >> web
> > > > >> > (gpu_burn and stress); I ran the two of them at the same time
> for
> > > two
> > > > 

Re: [gmx-users] Fwd: SIMD options

[Mark Abraham]

Hi,

There will have been reports by cmake about whether the detection program
compiled and/or ran successfully, which would be useful diagnostic
information. Please run cmake in a fresh build directory and look for that.
It is possible to run that program individually, if the issue is that it
compiles and fails to run somehow (e.g. that linking is broken)

Mark

On Thu, 12 Sep 2019 at 17:06, Stefano Guglielmo 
wrote:

> I cannot say about BIOS/firmware yet, I made a quite "standard"
> installation of centOS 7, but I'll try to check; as for cpu, for what it
> means, I made the stress test which brought up temperature for two hours
> together with gpu_burn, so I would exclude cooling failure.
>
> A further update: I yum-installed devtoolset-8-toolchain, so now cmake
> finds gcc 8.3.1, but again SIMD instructions detection failed.
> Sorry for bothering but I must say that I am getting a bit confused.
>
> Stefano
>
> <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> Mail
> priva di virus. www.avast.com
> <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> Il giorno gio 12 set 2019 alle ore 16:35 Szilárd Páll <
> pall.szil...@gmail.com> ha scritto:
>
> > On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo
> >  wrote:
> > >
> > > As an update, I have just tried a run with cpu only after compiling
> with
> > > AVX2_128 and the workstation turned off after few minutes.
> >
> > That is suspicious. Perhaps a CPU cooling issue? Otherwise you may
> > have a BIOS/firmware issue or, less likely but possibly, a a faulty
> > CPU.
> >
> > --
> > Szilárd
> >
> > > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > > Mail
> > > priva di virus. www.avast.com
> > > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > > <#m_360888458910571867_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > >
> > > Il giorno gio 12 set 2019 alle ore 15:19 Stefano Guglielmo <
> > > stefano.guglie...@unito.it> ha scritto:
> > >
> > > > Hi Szilard,
> > > > thanks for your reply.
> > > > The compiler is gcc 4.8.5.
> > > > I put below the link where you can find the files coming from cmake
> and
> > > > the output for "AUTO" SIMD instruction. As for cpu only, as you had
> > > > suggested previously I tried a run (after compiling with AVX2_256)
> and
> > it
> > > > worked without any problems for about 5 hours. I will try with
> > AVX2_128 as
> > > > well.
> > > >
> > > > Stefano
> > > >
> > > >
> >
> https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0
> > > >
> > > >
> > > > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> > Mail
> > > > priva di virus. www.avast.com
> > > > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > > >
> >
> <#m_360888458910571867_m_-3568712886600561053_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > >
> > > > Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll <
> > > > pall.szil...@gmail.com> ha scritto:
> > > >
> > > >> On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
> > > >>  wrote:
> > > >> >
> > > >> > I apologize for the mistake, there was a typo in the object that
> > could
> > > >> be
> > > >> > misleading, so I re-post with the correct object,
> > > >> > sorry.
> > > >> >
> > > >> > -- Forwarded message -
> > > >> > Da: Stefano Guglielmo 
> > > >> > Date: mer 11 set 2019 alle ore 17:17
> > > >> > Subject: SMD options
> > > >> > To: 
> > > >> >
> > > >> >
> > > >> > Hi all,
> > > >> > following my previous post regarding anomalous crashing of the
> > system on
> > > >> > running gromacs on two gpus, I have some new elements to add.
> > > >> > I tested the workstation with two tools for gpu and cpu I found on
> > the
> > > >> web
> > > >> > (gpu_burn and stress); I ran the two of them at the same time for
> > two
> > > >> hours
> > > >> > pushing both gpus (2 x 250 W) and cpu (250 W), and no error
> reports
> > or
> > > >> > overheating have resulted, so I would say that the hardware seems
> > to be
> > > >> > stable.
> > > >> > Despite this, I found something that perhaps could be not normal
> > during
> > > >> > gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD
> > > >> > instructions:  NONE"; in this condition I can run gromacs without
> > any
> > > >> > unexpected crash, even though a little less efficiently; setting
> > > >> -DGMX_SIMD
> > > >> > to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and
> > > >> > installation (with all the tests passed), but on running the
> sudden
> > > >> turning
> > > >> > off happens in the conditions I had described in the previous
> posts
> > > >> > (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> > > >> > 

Re: [gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

I cannot say about BIOS/firmware yet, I made a quite "standard"
installation of centOS 7, but I'll try to check; as for cpu, for what it
means, I made the stress test which brought up temperature for two hours
together with gpu_burn, so I would exclude cooling failure.

A further update: I yum-installed devtoolset-8-toolchain, so now cmake
finds gcc 8.3.1, but again SIMD instructions detection failed.
Sorry for bothering but I must say that I am getting a bit confused.

Stefano


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Il giorno gio 12 set 2019 alle ore 16:35 Szilárd Páll <
pall.szil...@gmail.com> ha scritto:

> On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo
>  wrote:
> >
> > As an update, I have just tried a run with cpu only after compiling with
> > AVX2_128 and the workstation turned off after few minutes.
>
> That is suspicious. Perhaps a CPU cooling issue? Otherwise you may
> have a BIOS/firmware issue or, less likely but possibly, a a faulty
> CPU.
>
> --
> Szilárd
>
> > <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> > Mail
> > priva di virus. www.avast.com
> > <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> > <#m_360888458910571867_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >
> > Il giorno gio 12 set 2019 alle ore 15:19 Stefano Guglielmo <
> > stefano.guglie...@unito.it> ha scritto:
> >
> > > Hi Szilard,
> > > thanks for your reply.
> > > The compiler is gcc 4.8.5.
> > > I put below the link where you can find the files coming from cmake and
> > > the output for "AUTO" SIMD instruction. As for cpu only, as you had
> > > suggested previously I tried a run (after compiling with AVX2_256) and
> it
> > > worked without any problems for about 5 hours. I will try with
> AVX2_128 as
> > > well.
> > >
> > > Stefano
> > >
> > >
> https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0
> > >
> > >
> > > <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
> Mail
> > > priva di virus. www.avast.com
> > > <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> > >
> <#m_360888458910571867_m_-3568712886600561053_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > >
> > > Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll <
> > > pall.szil...@gmail.com> ha scritto:
> > >
> > >> On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
> > >>  wrote:
> > >> >
> > >> > I apologize for the mistake, there was a typo in the object that
> could
> > >> be
> > >> > misleading, so I re-post with the correct object,
> > >> > sorry.
> > >> >
> > >> > -- Forwarded message -
> > >> > Da: Stefano Guglielmo 
> > >> > Date: mer 11 set 2019 alle ore 17:17
> > >> > Subject: SMD options
> > >> > To: 
> > >> >
> > >> >
> > >> > Hi all,
> > >> > following my previous post regarding anomalous crashing of the
> system on
> > >> > running gromacs on two gpus, I have some new elements to add.
> > >> > I tested the workstation with two tools for gpu and cpu I found on
> the
> > >> web
> > >> > (gpu_burn and stress); I ran the two of them at the same time for
> two
> > >> hours
> > >> > pushing both gpus (2 x 250 W) and cpu (250 W), and no error reports
> or
> > >> > overheating have resulted, so I would say that the hardware seems
> to be
> > >> > stable.
> > >> > Despite this, I found something that perhaps could be not normal
> during
> > >> > gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD
> > >> > instructions:  NONE"; in this condition I can run gromacs without
> any
> > >> > unexpected crash, even though a little less efficiently; setting
> > >> -DGMX_SIMD
> > >> > to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and
> > >> > installation (with all the tests passed), but on running the sudden
> > >> turning
> > >> > off happens in the conditions I had described in the previous posts
> > >> > (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> > >> > -gputasks 00 -pin on -pinoffset 0 -pinstride 1
> > >> > plus
> > >> > gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> > >> > -gputasks 11 -pin on -pinoffset 28 -pinstride 1)
> > >> > Do you think that there could be a relationship between SIMD options
> > >> > setting and the crash of the system?
> > >>
> > >> Unlikely, but not impossible. I would however expect that a CPU-only
> > >> GROMACS run would also lead to a crash. Can you try to do an AVX2_128
> > >> CPU-only run (e.g. mdrun -ntmpi 64 -ntomp 1 -nb cpu) and let it run
> > >> for a few hours?
> > >>
> > >> > Does anyone have any idea about the
> > >> > reason why gromacs does not seem to automatically 

Re: [gmx-users] Fwd: SIMD options

[Szilárd Páll]

On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo
 wrote:
>
> As an update, I have just tried a run with cpu only after compiling with
> AVX2_128 and the workstation turned off after few minutes.

That is suspicious. Perhaps a CPU cooling issue? Otherwise you may
have a BIOS/firmware issue or, less likely but possibly, a a faulty
CPU.

--
Szilárd

> 
> Mail
> priva di virus. www.avast.com
> 
> <#m_360888458910571867_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> Il giorno gio 12 set 2019 alle ore 15:19 Stefano Guglielmo <
> stefano.guglie...@unito.it> ha scritto:
>
> > Hi Szilard,
> > thanks for your reply.
> > The compiler is gcc 4.8.5.
> > I put below the link where you can find the files coming from cmake and
> > the output for "AUTO" SIMD instruction. As for cpu only, as you had
> > suggested previously I tried a run (after compiling with AVX2_256) and it
> > worked without any problems for about 5 hours. I will try with AVX2_128 as
> > well.
> >
> > Stefano
> >
> > https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0
> >
> >
> > 
> >  Mail
> > priva di virus. www.avast.com
> > 
> > <#m_360888458910571867_m_-3568712886600561053_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >
> > Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll <
> > pall.szil...@gmail.com> ha scritto:
> >
> >> On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
> >>  wrote:
> >> >
> >> > I apologize for the mistake, there was a typo in the object that could
> >> be
> >> > misleading, so I re-post with the correct object,
> >> > sorry.
> >> >
> >> > -- Forwarded message -
> >> > Da: Stefano Guglielmo 
> >> > Date: mer 11 set 2019 alle ore 17:17
> >> > Subject: SMD options
> >> > To: 
> >> >
> >> >
> >> > Hi all,
> >> > following my previous post regarding anomalous crashing of the system on
> >> > running gromacs on two gpus, I have some new elements to add.
> >> > I tested the workstation with two tools for gpu and cpu I found on the
> >> web
> >> > (gpu_burn and stress); I ran the two of them at the same time for two
> >> hours
> >> > pushing both gpus (2 x 250 W) and cpu (250 W), and no error reports or
> >> > overheating have resulted, so I would say that the hardware seems to be
> >> > stable.
> >> > Despite this, I found something that perhaps could be not normal during
> >> > gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD
> >> > instructions:  NONE"; in this condition I can run gromacs without any
> >> > unexpected crash, even though a little less efficiently; setting
> >> -DGMX_SIMD
> >> > to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and
> >> > installation (with all the tests passed), but on running the sudden
> >> turning
> >> > off happens in the conditions I had described in the previous posts
> >> > (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> >> > -gputasks 00 -pin on -pinoffset 0 -pinstride 1
> >> > plus
> >> > gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> >> > -gputasks 11 -pin on -pinoffset 28 -pinstride 1)
> >> > Do you think that there could be a relationship between SIMD options
> >> > setting and the crash of the system?
> >>
> >> Unlikely, but not impossible. I would however expect that a CPU-only
> >> GROMACS run would also lead to a crash. Can you try to do an AVX2_128
> >> CPU-only run (e.g. mdrun -ntmpi 64 -ntomp 1 -nb cpu) and let it run
> >> for a few hours?
> >>
> >> > Does anyone have any idea about the
> >> > reason why gromacs does not seem to automatically recognize any options
> >> for
> >> > my AMD threadripper? Can there be any solutions for this?
> >>
> >> That is certainly unexpected, perhaps there is an issue with your
> >> compler toolchains. What compiler are you using? Can you please share
> >> your cmake detection output and CMakeCache.txt?
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >> > Thanks again
> >> > Stefano
> >> > PS: the workstation is running with centOS 7 and aThreadripper 2990WX
> >> cpu.
> >> >
> >> > --
> >> > Stefano GUGLIELMO PhD
> >> > Assistant Professor of Medicinal Chemistry
> >> > Department of Drug Science and Technology
> >> > Via P. Giuria 9
> >> > 10125 Turin, ITALY
> >> > ph. +39 (0)11 6707178
> >> >
> >> >
> >> > <
> >> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >> >
> >> > Mail
> >> > priva di virus. www.avast.com
> >> > <
> >> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >> >
> >> > <#m_-7114857415897320041_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >> >
> >> >
> >> > --
> 

Re: [gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

As an update, I have just tried a run with cpu only after compiling with
AVX2_128 and the workstation turned off after few minutes.


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Il giorno gio 12 set 2019 alle ore 15:19 Stefano Guglielmo <
stefano.guglie...@unito.it> ha scritto:

> Hi Szilard,
> thanks for your reply.
> The compiler is gcc 4.8.5.
> I put below the link where you can find the files coming from cmake and
> the output for "AUTO" SIMD instruction. As for cpu only, as you had
> suggested previously I tried a run (after compiling with AVX2_256) and it
> worked without any problems for about 5 hours. I will try with AVX2_128 as
> well.
>
> Stefano
>
> https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0
>
>
> 
>  Mail
> priva di virus. www.avast.com
> 
> <#m_360888458910571867_m_-3568712886600561053_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll <
> pall.szil...@gmail.com> ha scritto:
>
>> On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
>>  wrote:
>> >
>> > I apologize for the mistake, there was a typo in the object that could
>> be
>> > misleading, so I re-post with the correct object,
>> > sorry.
>> >
>> > -- Forwarded message -
>> > Da: Stefano Guglielmo 
>> > Date: mer 11 set 2019 alle ore 17:17
>> > Subject: SMD options
>> > To: 
>> >
>> >
>> > Hi all,
>> > following my previous post regarding anomalous crashing of the system on
>> > running gromacs on two gpus, I have some new elements to add.
>> > I tested the workstation with two tools for gpu and cpu I found on the
>> web
>> > (gpu_burn and stress); I ran the two of them at the same time for two
>> hours
>> > pushing both gpus (2 x 250 W) and cpu (250 W), and no error reports or
>> > overheating have resulted, so I would say that the hardware seems to be
>> > stable.
>> > Despite this, I found something that perhaps could be not normal during
>> > gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD
>> > instructions:  NONE"; in this condition I can run gromacs without any
>> > unexpected crash, even though a little less efficiently; setting
>> -DGMX_SIMD
>> > to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and
>> > installation (with all the tests passed), but on running the sudden
>> turning
>> > off happens in the conditions I had described in the previous posts
>> > (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
>> > -gputasks 00 -pin on -pinoffset 0 -pinstride 1
>> > plus
>> > gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
>> > -gputasks 11 -pin on -pinoffset 28 -pinstride 1)
>> > Do you think that there could be a relationship between SIMD options
>> > setting and the crash of the system?
>>
>> Unlikely, but not impossible. I would however expect that a CPU-only
>> GROMACS run would also lead to a crash. Can you try to do an AVX2_128
>> CPU-only run (e.g. mdrun -ntmpi 64 -ntomp 1 -nb cpu) and let it run
>> for a few hours?
>>
>> > Does anyone have any idea about the
>> > reason why gromacs does not seem to automatically recognize any options
>> for
>> > my AMD threadripper? Can there be any solutions for this?
>>
>> That is certainly unexpected, perhaps there is an issue with your
>> compler toolchains. What compiler are you using? Can you please share
>> your cmake detection output and CMakeCache.txt?
>>
>> Cheers,
>> --
>> Szilárd
>>
>> > Thanks again
>> > Stefano
>> > PS: the workstation is running with centOS 7 and aThreadripper 2990WX
>> cpu.
>> >
>> > --
>> > Stefano GUGLIELMO PhD
>> > Assistant Professor of Medicinal Chemistry
>> > Department of Drug Science and Technology
>> > Via P. Giuria 9
>> > 10125 Turin, ITALY
>> > ph. +39 (0)11 6707178
>> >
>> >
>> > <
>> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
>> >
>> > Mail
>> > priva di virus. www.avast.com
>> > <
>> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
>> >
>> > <#m_-7114857415897320041_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>> >
>> >
>> > --
>> > Stefano GUGLIELMO PhD
>> > Assistant Professor of Medicinal Chemistry
>> > Department of Drug Science and Technology
>> > Via P. Giuria 9
>> > 10125 Turin, ITALY
>> > ph. +39 (0)11 6707178
>> > --
>> > 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 

Re: [gmx-users] Fwd: SIMD options

[Szilárd Páll]

On Thu, Sep 12, 2019 at 3:25 PM Stefano Guglielmo
 wrote:
>
>  Hi Szilard,
> thanks for your reply.
> The compiler is gcc 4.8.5.

That is ancient. From your cmake.out:

-- Detection for best SIMD instructions failed, using SIMD - None
-- SIMD instructions disabled

Update your compiler toolchain to a modern compiler (e.g. gcc 8),
you'll also get much better performance.

Cheers,
--
Szilárd

> I put below the link where you can find the files coming from cmake and the
> output for "AUTO" SIMD instruction. As for cpu only, as you had suggested
> previously I tried a run (after compiling with AVX2_256) and it worked
> without any problems for about 5 hours. I will try with AVX2_128 as well.
>
> Stefano
>
> https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0
>
> 
> Mail
> priva di virus. www.avast.com
> 
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll <
> pall.szil...@gmail.com> ha scritto:
>
> > On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
> >  wrote:
> > >
> > > I apologize for the mistake, there was a typo in the object that could be
> > > misleading, so I re-post with the correct object,
> > > sorry.
> > >
> > > -- Forwarded message -
> > > Da: Stefano Guglielmo 
> > > Date: mer 11 set 2019 alle ore 17:17
> > > Subject: SMD options
> > > To: 
> > >
> > >
> > > Hi all,
> > > following my previous post regarding anomalous crashing of the system on
> > > running gromacs on two gpus, I have some new elements to add.
> > > I tested the workstation with two tools for gpu and cpu I found on the
> > web
> > > (gpu_burn and stress); I ran the two of them at the same time for two
> > hours
> > > pushing both gpus (2 x 250 W) and cpu (250 W), and no error reports or
> > > overheating have resulted, so I would say that the hardware seems to be
> > > stable.
> > > Despite this, I found something that perhaps could be not normal during
> > > gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD
> > > instructions:  NONE"; in this condition I can run gromacs without any
> > > unexpected crash, even though a little less efficiently; setting
> > -DGMX_SIMD
> > > to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and
> > > installation (with all the tests passed), but on running the sudden
> > turning
> > > off happens in the conditions I had described in the previous posts
> > > (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> > > -gputasks 00 -pin on -pinoffset 0 -pinstride 1
> > > plus
> > > gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> > > -gputasks 11 -pin on -pinoffset 28 -pinstride 1)
> > > Do you think that there could be a relationship between SIMD options
> > > setting and the crash of the system?
> >
> > Unlikely, but not impossible. I would however expect that a CPU-only
> > GROMACS run would also lead to a crash. Can you try to do an AVX2_128
> > CPU-only run (e.g. mdrun -ntmpi 64 -ntomp 1 -nb cpu) and let it run
> > for a few hours?
> >
> > > Does anyone have any idea about the
> > > reason why gromacs does not seem to automatically recognize any options
> > for
> > > my AMD threadripper? Can there be any solutions for this?
> >
> > That is certainly unexpected, perhaps there is an issue with your
> > compler toolchains. What compiler are you using? Can you please share
> > your cmake detection output and CMakeCache.txt?
> >
> > Cheers,
> > --
> > Szilárd
> >
> > > Thanks again
> > > Stefano
> > > PS: the workstation is running with centOS 7 and aThreadripper 2990WX
> > cpu.
> > >
> > > --
> > > Stefano GUGLIELMO PhD
> > > Assistant Professor of Medicinal Chemistry
> > > Department of Drug Science and Technology
> > > Via P. Giuria 9
> > > 10125 Turin, ITALY
> > > ph. +39 (0)11 6707178
> > >
> > >
> > > <
> > https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > > Mail
> > > priva di virus. www.avast.com
> > > <
> > https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> > >
> > > <#m_-7114857415897320041_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > >
> > >
> > > --
> > > Stefano GUGLIELMO PhD
> > > Assistant Professor of Medicinal Chemistry
> > > Department of Drug Science and Technology
> > > Via P. Giuria 9
> > > 10125 Turin, ITALY
> > > ph. +39 (0)11 6707178
> > > --
> > > 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.
> > 

Re: [gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

 Hi Szilard,
thanks for your reply.
The compiler is gcc 4.8.5.
I put below the link where you can find the files coming from cmake and the
output for "AUTO" SIMD instruction. As for cpu only, as you had suggested
previously I tried a run (after compiling with AVX2_256) and it worked
without any problems for about 5 hours. I will try with AVX2_128 as well.

Stefano

https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0


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<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll <
pall.szil...@gmail.com> ha scritto:

> On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
>  wrote:
> >
> > I apologize for the mistake, there was a typo in the object that could be
> > misleading, so I re-post with the correct object,
> > sorry.
> >
> > -- Forwarded message -
> > Da: Stefano Guglielmo 
> > Date: mer 11 set 2019 alle ore 17:17
> > Subject: SMD options
> > To: 
> >
> >
> > Hi all,
> > following my previous post regarding anomalous crashing of the system on
> > running gromacs on two gpus, I have some new elements to add.
> > I tested the workstation with two tools for gpu and cpu I found on the
> web
> > (gpu_burn and stress); I ran the two of them at the same time for two
> hours
> > pushing both gpus (2 x 250 W) and cpu (250 W), and no error reports or
> > overheating have resulted, so I would say that the hardware seems to be
> > stable.
> > Despite this, I found something that perhaps could be not normal during
> > gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD
> > instructions:  NONE"; in this condition I can run gromacs without any
> > unexpected crash, even though a little less efficiently; setting
> -DGMX_SIMD
> > to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and
> > installation (with all the tests passed), but on running the sudden
> turning
> > off happens in the conditions I had described in the previous posts
> > (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> > -gputasks 00 -pin on -pinoffset 0 -pinstride 1
> > plus
> > gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> > -gputasks 11 -pin on -pinoffset 28 -pinstride 1)
> > Do you think that there could be a relationship between SIMD options
> > setting and the crash of the system?
>
> Unlikely, but not impossible. I would however expect that a CPU-only
> GROMACS run would also lead to a crash. Can you try to do an AVX2_128
> CPU-only run (e.g. mdrun -ntmpi 64 -ntomp 1 -nb cpu) and let it run
> for a few hours?
>
> > Does anyone have any idea about the
> > reason why gromacs does not seem to automatically recognize any options
> for
> > my AMD threadripper? Can there be any solutions for this?
>
> That is certainly unexpected, perhaps there is an issue with your
> compler toolchains. What compiler are you using? Can you please share
> your cmake detection output and CMakeCache.txt?
>
> Cheers,
> --
> Szilárd
>
> > Thanks again
> > Stefano
> > PS: the workstation is running with centOS 7 and aThreadripper 2990WX
> cpu.
> >
> > --
> > Stefano GUGLIELMO PhD
> > Assistant Professor of Medicinal Chemistry
> > Department of Drug Science and Technology
> > Via P. Giuria 9
> > 10125 Turin, ITALY
> > ph. +39 (0)11 6707178
> >
> >
> > <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> > Mail
> > priva di virus. www.avast.com
> > <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >
> > <#m_-7114857415897320041_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >
> >
> > --
> > Stefano GUGLIELMO PhD
> > Assistant Professor of Medicinal Chemistry
> > Department of Drug Science and Technology
> > Via P. Giuria 9
> > 10125 Turin, ITALY
> > ph. +39 (0)11 6707178
> > --
> > 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!
>
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-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178
-- 
Gromacs Users 

Re: [gmx-users] Fwd: SIMD options

[Szilárd Páll]

On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
 wrote:
>
> I apologize for the mistake, there was a typo in the object that could be
> misleading, so I re-post with the correct object,
> sorry.
>
> -- Forwarded message -
> Da: Stefano Guglielmo 
> Date: mer 11 set 2019 alle ore 17:17
> Subject: SMD options
> To: 
>
>
> Hi all,
> following my previous post regarding anomalous crashing of the system on
> running gromacs on two gpus, I have some new elements to add.
> I tested the workstation with two tools for gpu and cpu I found on the web
> (gpu_burn and stress); I ran the two of them at the same time for two hours
> pushing both gpus (2 x 250 W) and cpu (250 W), and no error reports or
> overheating have resulted, so I would say that the hardware seems to be
> stable.
> Despite this, I found something that perhaps could be not normal during
> gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD
> instructions:  NONE"; in this condition I can run gromacs without any
> unexpected crash, even though a little less efficiently; setting -DGMX_SIMD
> to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and
> installation (with all the tests passed), but on running the sudden turning
> off happens in the conditions I had described in the previous posts
> (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> -gputasks 00 -pin on -pinoffset 0 -pinstride 1
> plus
> gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> -gputasks 11 -pin on -pinoffset 28 -pinstride 1)
> Do you think that there could be a relationship between SIMD options
> setting and the crash of the system?

Unlikely, but not impossible. I would however expect that a CPU-only
GROMACS run would also lead to a crash. Can you try to do an AVX2_128
CPU-only run (e.g. mdrun -ntmpi 64 -ntomp 1 -nb cpu) and let it run
for a few hours?

> Does anyone have any idea about the
> reason why gromacs does not seem to automatically recognize any options for
> my AMD threadripper? Can there be any solutions for this?

That is certainly unexpected, perhaps there is an issue with your
compler toolchains. What compiler are you using? Can you please share
your cmake detection output and CMakeCache.txt?

Cheers,
--
Szilárd

> Thanks again
> Stefano
> PS: the workstation is running with centOS 7 and aThreadripper 2990WX cpu.
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
>
>
> 
> Mail
> priva di virus. www.avast.com
> 
> <#m_-7114857415897320041_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
> --
> 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.
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[gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

I apologize for the mistake, there was a typo in the object that could be
misleading, so I re-post with the correct object,
sorry.

-- Forwarded message -
Da: Stefano Guglielmo 
Date: mer 11 set 2019 alle ore 17:17
Subject: SMD options
To: 


Hi all,
following my previous post regarding anomalous crashing of the system on
running gromacs on two gpus, I have some new elements to add.
I tested the workstation with two tools for gpu and cpu I found on the web
(gpu_burn and stress); I ran the two of them at the same time for two hours
pushing both gpus (2 x 250 W) and cpu (250 W), and no error reports or
overheating have resulted, so I would say that the hardware seems to be
stable.
Despite this, I found something that perhaps could be not normal during
gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD
instructions:  NONE"; in this condition I can run gromacs without any
unexpected crash, even though a little less efficiently; setting -DGMX_SIMD
to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and
installation (with all the tests passed), but on running the sudden turning
off happens in the conditions I had described in the previous posts
(gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
-gputasks 00 -pin on -pinoffset 0 -pinstride 1
plus
gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
-gputasks 11 -pin on -pinoffset 28 -pinstride 1)
Do you think that there could be a relationship between SIMD options
setting and the crash of the system? Does anyone have any idea about the
reason why gromacs does not seem to automatically recognize any options for
my AMD threadripper? Can there be any solutions for this?
Thanks again
Stefano
PS: the workstation is running with centOS 7 and aThreadripper 2990WX cpu.

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178



Mail
priva di virus. www.avast.com

<#m_-7114857415897320041_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>


-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178
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[gmx-users] Fwd: query

[Nirali Desai]

Hello,

I want to calculate the energy of the two groups. I have defined those
groups in mdp file. I want to run it for 5 ns. So, I set the nsteps and all
parameters according to my need. Now I am using the rerun command for
calculating the energy. But it is only giving the energies till 100 ps and
not more than that. Please help me on this and guide me on  this problem.

using following commands:

1. Making index file according to the atoms: like a 1-15 PROA..etc like
for  PROB and PROC and then changing the energy groups in mdout.mdp file.
Any two groups at a time. (PROA, B,C= groups)
2. gmx grompp -f mdout.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -n
index.ndx -o ie.tpr
3. gmx mdrun -deffnm -ie -rerun md.xtc
4. gmx energy -f ie.edr -s ie.tpr -o energy.xvg
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Re: [gmx-users] Fwd: Simulation blowing up in parallel (h-bonds constraints)

[John Whittaker]

Hi Jan,

> Dear gromacs-users,
>
> I am encountering a puzzling problem with my simulation of a simple
> protein (~2.000 atoms, only standard amino acids, Calcium cofactor) in
> tip3p water (~10.000 molecules) using the amber99sb-ildn force field and
> lincs constraints set to "h-bonds". When I try to run the production on
> more than one MPI rank, the simulation fails with errors like:
>
> Fatal error:
> 80 particles communicated to PME rank 1 are more than 2/3 times the
> cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
>
> Or warnings like:
>
> WARNING: Listed nonbonded interaction between particles 224 and 235
> at distance 3.720 which is larger than the table limit 2.569 nm.

When you got this ^ error, did you visualize your trajectory and check
what was up with these particular particles? Maybe that could give you
some clues about what's happening.

By the way, the mailing list doesn't support attachments. If you want to
share a file, you either have to copy/paste it in the email or upload it
to a file-sharing website (e.g. Dropbox).

- John


>
> (see run_hbonds_tight_parallel.log)
>
>
> I am quite sure that my system is well equilibrated, though (correct me,
> if I am mistaken here). The problem could not be resolved by using a
> very strict preparation protocol of the system (.mdp files attached),
> using a 1 fs timestep and high lincs (iter 2, order 6) accuracy:
>
>   - steepest decent minimisation (emtol 100 kJ/mol) in vacuum
>
>   - solvation, neutralisation
>
>   - steepest decent minimisation (emtol 100 kJ/mol)
>
>   - conjugate gradient minimisation (emtol 1 kJ/mol, not reached though
> in single precision)
>
>   - NVT eq. 300K (v-rescale tau_t 0.1, coupling groups
> protein/non-protein, all-bonds constraints, position restraints on the
> protein) 300 ps
>
>   - NPT eq. (Berendsen, tau_p 1, all-bonds constraints, position
> restraints on the protein) 300 ps
>
>   - NPT 2 eq. (no position restraints on the protein) 300 ps
>
>   - NPT 3 eq. (switching to h-bond constraints) 400 ps
>
>   - NPT 4 eq. (switching to Parrinello-Rahman) 400 ps
>
> Temperature, pressure, density and potential show reasonable
> fluctuations, I think, during the last run:
>
> Energy  Average   Err.Est.   RMSD Tot-Drift
> ---
> Potential   -534764 39    766.653 5.78602 (kJ/mol)
>
> Density 1002.32    0.2    2.49712 -1.27332 
> (kg/m^3)
>
> Temperature 299.931  0.061    1.61166 0.0932882  (K)
>
> Pressure   -1.90648    0.8    120.449 2.49509 (bar)
>
> I can not spot any geometrical clashes in the system. Keeping the 1 fs
> timestep and high lincs accuracy also during production does not help
> (as well as decreasing shake-tol and verlet-buffer-tolerance). Switching
> back to all-bonds constraints, however, allows a parallel run again. The
> simulation with h-bonds constraints runs only stable, if run serial on
> one node (only OpenMP thread usage).
>
> I'd like to keep the h-bonds constraints because switching to all-bonds
> is discouraged by gromacs for the used force field:
>
> NOTE 1 [file unknown]:
>    You are using constraints on all bonds, whereas the forcefield has been
>    parametrized only with constraints involving hydrogen atoms. We suggest
>    using constraints = h-bonds instead, this will also improve
> performance.
>
> Any suggestions on how to achieve a MPI parallel run with this system
> keeping the h-bonds constraints or advice on better equilibration are
> highly appreciated.
>
> Thank you for your help!
>
> Best regards
> Jan
>
>
>
>
>
> --
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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[gmx-users] Fwd: Simulation blowing up in parallel (h-bonds constraints)

[jan . joswig]

Dear gromacs-users,

I am encountering a puzzling problem with my simulation of a simple 
protein (~2.000 atoms, only standard amino acids, Calcium cofactor) in 
tip3p water (~10.000 molecules) using the amber99sb-ildn force field and 
lincs constraints set to "h-bonds". When I try to run the production on 
more than one MPI rank, the simulation fails with errors like:


Fatal error:
80 particles communicated to PME rank 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

Or warnings like:

WARNING: Listed nonbonded interaction between particles 224 and 235
at distance 3.720 which is larger than the table limit 2.569 nm.

(see run_hbonds_tight_parallel.log)


I am quite sure that my system is well equilibrated, though (correct me, 
if I am mistaken here). The problem could not be resolved by using a 
very strict preparation protocol of the system (.mdp files attached), 
using a 1 fs timestep and high lincs (iter 2, order 6) accuracy:


 - steepest decent minimisation (emtol 100 kJ/mol) in vacuum

 - solvation, neutralisation

 - steepest decent minimisation (emtol 100 kJ/mol)

 - conjugate gradient minimisation (emtol 1 kJ/mol, not reached though 
in single precision)


 - NVT eq. 300K (v-rescale tau_t 0.1, coupling groups 
protein/non-protein, all-bonds constraints, position restraints on the 
protein) 300 ps


 - NPT eq. (Berendsen, tau_p 1, all-bonds constraints, position 
restraints on the protein) 300 ps


 - NPT 2 eq. (no position restraints on the protein) 300 ps

 - NPT 3 eq. (switching to h-bond constraints) 400 ps

 - NPT 4 eq. (switching to Parrinello-Rahman) 400 ps

Temperature, pressure, density and potential show reasonable 
fluctuations, I think, during the last run:


Energy  Average   Err.Est.   RMSD Tot-Drift
---
Potential   -534764 39    766.653 5.78602 (kJ/mol)

Density 1002.32    0.2    2.49712 -1.27332  (kg/m^3)

Temperature 299.931  0.061    1.61166 0.0932882  (K)

Pressure   -1.90648    0.8    120.449 2.49509 (bar)

I can not spot any geometrical clashes in the system. Keeping the 1 fs 
timestep and high lincs accuracy also during production does not help 
(as well as decreasing shake-tol and verlet-buffer-tolerance). Switching 
back to all-bonds constraints, however, allows a parallel run again. The 
simulation with h-bonds constraints runs only stable, if run serial on 
one node (only OpenMP thread usage).


I'd like to keep the h-bonds constraints because switching to all-bonds 
is discouraged by gromacs for the used force field:


NOTE 1 [file unknown]:
  You are using constraints on all bonds, whereas the forcefield has been
  parametrized only with constraints involving hydrogen atoms. We suggest
  using constraints = h-bonds instead, this will also improve performance.

Any suggestions on how to achieve a MPI parallel run with this system 
keeping the h-bonds constraints or advice on better equilibration are 
highly appreciated.


Thank you for your help!

Best regards
Jan





;
;   File 'nopull_tight/mdout.mdp' was generated
;   By user: janjoswig (214764)
;   On host: qcm07
;   At date: Tue Aug 20 10:34:56 2019
;
;   Created by:
;:-) GROMACS - gmx grompp, 2019.1 (-:
;   
;   Executable:   /home/janjoswig/local/gromacs-2019.1/bin/gmx19
;   Data prefix:  /home/janjoswig/local/gromacs-2019.1
;   Working dir:  /home/janjoswig/Projects/Langerin/h3/setup
;   Command line:
; gmx grompp -f mdp.mdp -c npt4.gro -t npt4.cpt -p topol.top -o 
nopull_tight/run.tpr -r npt4.gro -po nopull_tight/mdout.mdp

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include  = 
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define   = 

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 1
; For exact run continuation or redoing part of a run
init-step= 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part  = 1
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 100
; group(s) for center of mass motion removal
comm-grps= 

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = -1

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 10
emstep   = 

Re: [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs

[Dallas Warren]

This shows why posting the entire output is important.  The note is
not the reason why grompp failed, the warning is what you need to take
note of and respond to/deal with.  If you are doing the step here to
add the counter-ions to neutralise charge, then do as the information
at the bottom is telling you to do, ignore the warning and proceed.

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 Mon, 24 Jun 2019 at 18:54, kalpana  wrote:
>
> Thanks a lot for your prompt response. I thought the fetal error is due to
> as its saying non-interger charge but i am not getting the output file to
> add ions to neutralize charge. The complete report is this:
>
>   gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr
>
> Setting the LD random seed to -1944004748
> Generated 330891 of the 330891 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 330891 of the 330891 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 1 [file topol.top, line 60959]:
>   System has non-zero total charge: -13.00
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
>
>
>
> WARNING 1 [file topol.top, line 60959]:
>   You are using Ewald electrostatics in a system with net charge. This can
>   lead to severe artifacts, such as ions moving into regions with low
>   dielectric, due to the uniform background charge. We suggest to
>   neutralize your system with counter ions, possibly in combination with a
>   physiological salt concentration.
>
>
>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
> J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
> Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a
> Net
> Charge
> J. Chem. Theory Comput. 10 (2014) pp. 381-393
>   --- Thank You ---  
>
> Cleaning up constraints and constant bonded interactions with virtual sites
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are:   424Protein residues
> There are: 16324  Water residues
> Analysing Protein...
> Number of degrees of freedom in T-Coupling group rest is 117267.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 80x80x80, spacing 0.116 0.116 0.116
> Estimate for the relative computational load of the PME mesh part: 0.26
> This run will generate roughly 6 Mb of data
>
> There was 1 note
>
> There was 1 warning
>
> ---
> Program: gmx grompp, version 2019.3
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2315)
>
> Fatal error:
> Too many warnings (1).
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> On Mon, Jun 24, 2019 at 11:22 AM Bratin Kumar Das <
> 177cy500.bra...@nitk.edu.in> wrote:
>
> > It is telling that system have -13 charge...Which need to be neutralise by
> > gmx genion command
> >
> > On Mon 24 Jun, 2019, 11:09 AM Alex,  wrote:
> >
> > > It is not an error message, but a note. If grompp quits with an error,
> > > please read it carefully.
> > >
> > > Alex
> > >
> > > On 6/23/2019 11:27 PM, kalpana wrote:
> > > > Kindly help to understand this error message becz with previous
> > > > installation with same setting files, there was no error. The error
> > > message
> > > > is as follows:
> > > >
> > > >gmx grompp -f  ions.mdp -c model1_solv.gro -p topol.top
> > -o
> > > > ions.tpr
> > > >
> > > >Setting the LD random seed to 31221519
> > > >Generated 330891 of the 330891 non-bonded parameter
> > > > combinations
> > > >Generating 1-4 interactions: fudge = 0.5
> > > >Generated 330891 of the 330891 1-4 parameter
> > combinations
> > > >Excluding 3 bonded neighbours molecule type
> > > 'Protein_chain_A'
> > > >Excluding 2 bonded neighbours molecule type 'SOL'
> > > >
> > > >NOTE 1 [file topol.top, line 60959]:
> > > >System has non-zero total charge: -13.00
> > > >Total charge should normally be an integer. See
> > > >
> > > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > > >for discussion on how close it should be to an integer.
> > > >
> > > > Best regards
> > > > Kalpana
> > > --
> > 

Re: [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs

[kalpana]

Thanks a lot for your prompt response. I thought the fetal error is due to
as its saying non-interger charge but i am not getting the output file to
add ions to neutralize charge. The complete report is this:

  gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr

Setting the LD random seed to -1944004748
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file topol.top, line 60959]:
  System has non-zero total charge: -13.00
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.




WARNING 1 [file topol.top, line 60959]:
  You are using Ewald electrostatics in a system with net charge. This can
  lead to severe artifacts, such as ions moving into regions with low
  dielectric, due to the uniform background charge. We suggest to
  neutralize your system with counter ions, possibly in combination with a
  physiological salt concentration.


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a
Net
Charge
J. Chem. Theory Comput. 10 (2014) pp. 381-393
  --- Thank You ---  

Cleaning up constraints and constant bonded interactions with virtual sites
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   424Protein residues
There are: 16324  Water residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 117267.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x80x80, spacing 0.116 0.116 0.116
Estimate for the relative computational load of the PME mesh part: 0.26
This run will generate roughly 6 Mb of data

There was 1 note

There was 1 warning

---
Program: gmx grompp, version 2019.3
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2315)

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

On Mon, Jun 24, 2019 at 11:22 AM Bratin Kumar Das <
177cy500.bra...@nitk.edu.in> wrote:

> It is telling that system have -13 charge...Which need to be neutralise by
> gmx genion command
>
> On Mon 24 Jun, 2019, 11:09 AM Alex,  wrote:
>
> > It is not an error message, but a note. If grompp quits with an error,
> > please read it carefully.
> >
> > Alex
> >
> > On 6/23/2019 11:27 PM, kalpana wrote:
> > > Kindly help to understand this error message becz with previous
> > > installation with same setting files, there was no error. The error
> > message
> > > is as follows:
> > >
> > >gmx grompp -f  ions.mdp -c model1_solv.gro -p topol.top
> -o
> > > ions.tpr
> > >
> > >Setting the LD random seed to 31221519
> > >Generated 330891 of the 330891 non-bonded parameter
> > > combinations
> > >Generating 1-4 interactions: fudge = 0.5
> > >Generated 330891 of the 330891 1-4 parameter
> combinations
> > >Excluding 3 bonded neighbours molecule type
> > 'Protein_chain_A'
> > >Excluding 2 bonded neighbours molecule type 'SOL'
> > >
> > >NOTE 1 [file topol.top, line 60959]:
> > >System has non-zero total charge: -13.00
> > >Total charge should normally be an integer. See
> > >
> > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > >for discussion on how close it should be to an integer.
> > >
> > > Best regards
> > > Kalpana
> > --
> > 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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> > 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] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs

[Dallas Warren]

A good place to always check for a GROMACS error is
http://manual.gromacs.org/current/user-guide/run-time-errors.html

Particular entry you want is:
http://manual.gromacs.org/current/user-guide/run-time-errors.html#system-has-non-zero-total-charge

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 Mon, 24 Jun 2019 at 15:30, kalpana  wrote:
>
> Kindly help to understand this error message becz with previous
> installation with same setting files, there was no error. The error message
> is as follows:
>
>   gmx grompp -f  ions.mdp -c model1_solv.gro -p topol.top -o
> ions.tpr
>
>   Setting the LD random seed to 31221519
>   Generated 330891 of the 330891 non-bonded parameter
> combinations
>   Generating 1-4 interactions: fudge = 0.5
>   Generated 330891 of the 330891 1-4 parameter combinations
>   Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>   Excluding 2 bonded neighbours molecule type 'SOL'
>
>   NOTE 1 [file topol.top, line 60959]:
>   System has non-zero total charge: -13.00
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
> Best regards
> Kalpana
> --
> 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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>
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Re: [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs

[Bratin Kumar Das]

It is telling that system have -13 charge...Which need to be neutralise by
gmx genion command

On Mon 24 Jun, 2019, 11:09 AM Alex,  wrote:

> It is not an error message, but a note. If grompp quits with an error,
> please read it carefully.
>
> Alex
>
> On 6/23/2019 11:27 PM, kalpana wrote:
> > Kindly help to understand this error message becz with previous
> > installation with same setting files, there was no error. The error
> message
> > is as follows:
> >
> >gmx grompp -f  ions.mdp -c model1_solv.gro -p topol.top -o
> > ions.tpr
> >
> >Setting the LD random seed to 31221519
> >Generated 330891 of the 330891 non-bonded parameter
> > combinations
> >Generating 1-4 interactions: fudge = 0.5
> >Generated 330891 of the 330891 1-4 parameter combinations
> >Excluding 3 bonded neighbours molecule type
> 'Protein_chain_A'
> >Excluding 2 bonded neighbours molecule type 'SOL'
> >
> >NOTE 1 [file topol.top, line 60959]:
> >System has non-zero total charge: -13.00
> >Total charge should normally be an integer. See
> >
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> >for discussion on how close it should be to an integer.
> >
> > Best regards
> > Kalpana
> --
> 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] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs

[Alex]

It is not an error message, but a note. If grompp quits with an error, 
please read it carefully.


Alex

On 6/23/2019 11:27 PM, kalpana wrote:

Kindly help to understand this error message becz with previous
installation with same setting files, there was no error. The error message
is as follows:

   gmx grompp -f  ions.mdp -c model1_solv.gro -p topol.top -o
ions.tpr

   Setting the LD random seed to 31221519
   Generated 330891 of the 330891 non-bonded parameter
combinations
   Generating 1-4 interactions: fudge = 0.5
   Generated 330891 of the 330891 1-4 parameter combinations
   Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
   Excluding 2 bonded neighbours molecule type 'SOL'

   NOTE 1 [file topol.top, line 60959]:
   System has non-zero total charge: -13.00
   Total charge should normally be an integer. See
   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer.

Best regards
Kalpana

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[gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs

[kalpana]

Kindly help to understand this error message becz with previous
installation with same setting files, there was no error. The error message
is as follows:

  gmx grompp -f  ions.mdp -c model1_solv.gro -p topol.top -o
ions.tpr

  Setting the LD random seed to 31221519
  Generated 330891 of the 330891 non-bonded parameter
combinations
  Generating 1-4 interactions: fudge = 0.5
  Generated 330891 of the 330891 1-4 parameter combinations
  Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
  Excluding 2 bonded neighbours molecule type 'SOL'

  NOTE 1 [file topol.top, line 60959]:
  System has non-zero total charge: -13.00
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

Best regards
Kalpana
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[gmx-users] Fwd: Calculating electron density profile of a lipid bilayer system

[Azadeh Alavizargar]

Dear Gromacs users

I am trying to calculate the electron density profiles of a lipid bilayer
system. However I am not getting the correct profile. I would appreciate it
a lot if you can help me.

Following is the procedure I go through:

1- first I create a ndx file to select the resnames:

gmx select -f trj_file.trr -s tpr_file.tpr -on index_file.ndx -select
'(resname DPPC TIP3)'

2- Then I created the electron.dat file including all the atoms (including
hydrogens) of the selected atoms. The first lines look like this:
208
OH = 8
H1 = 1
H2 = 1
N = 7
C13 = 6
H13A = 1
H13B = 1
H13C = 1
C14 = 6
H14A = 1
H14B = 1
H14C = 1
C15 = 6
...

3- Then I use gmx density in order to calculate the electron density of the
selected resnames:

gmx density -f trj_file.trr -s tpr_file.tpr -n index_file.ndx -o
 density_traj_center.xvg -dens electron -ei electron.dat -center -relative

However,  what I get is not similar to the ones in papers:
Best regards,
Azadeh
[image: image.png]
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[gmx-users] Fwd: [Gmx-plumed Query] - Lincs warnings during meta-dynamics calculation of pyranose sugar using phi and theta as Collective Variables

[Amit Singh]

I am doing meta-dynamics MD simulations of alpha-mannose using
GROMACS-PLUMED software. My collective variables are phi and theta
(Cremer-Pople ring puckering coordinates). But my simulations are
terminating prematurely with following LINCS warnings :


Step 464363, time 464.363 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.575117, max 12.384567 (between atoms 8 and 9)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  8  9  153.00.3415   1.4870  0.
  8  9  153.00.3415   1.4870  0.
  8  9  153.00.3415   1.4870  0.
  8  9  153.00.3415   1.4870  0.
  8  9  153.00.3415   1.4870  0.
  8  9  153.00.3415   1.4870  0.

My system has one alpha-mannose (atom no. 1 to 24) and 590 water molecules.
Respective .mdp file and plumed input file provided below:


***
title   = Production Run
; Run parameters
integrator= md; leap-frog integrator
nsteps = 5000; 1 * 5000 =
5 ps (50 ns)
dt= 0.001 ; 1 fs
; Output control
nstenergy= 5000  ; save energies every
5.0 ps
nstlog  = 5000  ; update log file
every 5.0 ps
nstxout-compressed   = 5000  ; save compressed coordinates
every 5.0 ps
compressed-x-grps = System; save the whole system
; Bond parameters
continuation= yes   ; Restarting after NPT
constraint_algorithm   = lincs; holonomic constraints
constraints  = h-bonds   ; bonds involving H
are constrained
lincs_iter = 2 ; accuracy of LINCS
lincs_order  = 4 ; also related to
accuracy
lincs-warnangle = 90
; Neighborsearching
cutoff-scheme   = Verlet; Buffered neighbor
searching
ns_type = grid  ; search neighboring
grid cells
nstlist= 20; 20 fs, largely
irrelevant with Verlet scheme
rcoulomb  = 1  ;  short-range electrostatic
cutoff (in nm)
rvdw = 1   ; short-range van der
Waals cutoff (in nm)
; Electrostatics
coulombtype  = PME   ; Particle Mesh Ewald for
long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing= 0.5  ; grid spacing for FFT
; Temperature coupling is on
tcoupl= v-rescale; modified
Berendsen thermostat
tc-grps   = AMAN Water  ; two coupling
groups - more accurate
tau_t  = 0.1   0.1   ; time
constant, in ps
ref_t   = 300   300  ;
reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl= Berendsen ;  Pressure
coupling on in NPT
pcoupltype = isotropic ; uniform
scaling of box vectors
tau_p  = 1.0   ; time
constant, in ps
ref_p  = 1.0   ; reference
pressure, in bar
compressibility   = 4.5e-5; isothermal
compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW
scheme
; Velocity generation
gen_vel = no; Velocity generation is off
; Comm removal
comm-mode  =  Linear
comm-grps=  AMAN Water

**

Plum.dat file

**
# Defining serial number of ring atoms from O5-C1-C2-C3-C4-C5

PUCKERING ATOMS=7,1,8,12,16,5 LABEL=puck

# Deposit a Gaussian every 600 time steps, with initial height equal to 1.0
kJ/mol

metad: METAD ARG=puck.phi,puck.theta SIGMA=0.35,0.35 PACE=600 HEIGHT=1.0
BIASFACTOR=10.0 TEMP=300.0 FILE=HILLS_1

# Print both collective variables and the value of the bias potential on
COLVAR file
PRINT ARG=puck.phi,puck.theta FILE=COLVAR_1 STRIDE=10

***

I had gone through the gromacs web-page (

Re: [gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

[ISHRAT JAHAN]

Thank you Justin sir for the reply. I have resolved my problem.

On Wed, May 8, 2019, 5:57 PM Justin Lemkul  wrote:

>
>
> On 5/7/19 1:41 AM, ISHRAT JAHAN wrote:
> > -- Forwarded message -
> > From: ISHRAT JAHAN 
> > Date: Tue, May 7, 2019 at 11:05 AM
> > Subject: atoms are not part of any of the T-Coupling groups
> > To: 
> >
> >
> > Dear all,
> > I am trying to calculate the lennard Jones interaction energy between
> > protein and urea in the first solvation shell. I have made the index
> group
> > of urea molecule in the first solvation shell and then tried to generate
> > the .tpr file using that index. After running the command
> > gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o
> > prot_u3M_rerun -n water_urea_5ofprot.ndx
> > following error occur-
> > 35099 atoms are not part of any of the T-Coupling groups
> > part of  .mdp file and index file is given below
> > rvdw=  1.2^M
> > fourierspacing = 0.12^M
> > fourier_nx = 0^M
> > fourier_ny = 0^M
> > fourier_nz = 0^M
> > pme_order = 4^M
> > ewald_rtol = 1e-5^M
> > optimize_fft = yes^M
> > ; Berendsen temperature coupling is on in two groups^M
> > Tcoupl  =  V-rescale^M
> > tc-grps =  Protein   Urea_5ofprot^M
> > tau_t   =  0.10.1 ^M
> > ref_t   =  300300   ^M
> > ; Energy monitoring^M
> > energygrps  =  Protein  Urea_5ofprot
> > ; Isotropic pressure coupling is now on^M
> > Pcoupl  =  berendsen^M
> >   and at the end of the Index file i have only added the residue index of
> > urea within 5 of protein and save the index file.
>
> While you can define whatever energygrps you like (note that the
> molecules will change over time and your results may end up being not
> useful), you need to couple all atoms in the system to a thermostat via
> tc-grps. Your urea selection is only a subset of the urea molecules, and
> if you have any other solvent, ions, etc. they are not being accounted
> for. tc-grps = Protein Non-Protein is almost always the way to go.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
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> posting!
>
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>
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Re: [gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

[Justin Lemkul]

On 5/7/19 1:41 AM, ISHRAT JAHAN wrote:

-- Forwarded message -
From: ISHRAT JAHAN 
Date: Tue, May 7, 2019 at 11:05 AM
Subject: atoms are not part of any of the T-Coupling groups
To: 


Dear all,
I am trying to calculate the lennard Jones interaction energy between
protein and urea in the first solvation shell. I have made the index group
of urea molecule in the first solvation shell and then tried to generate
the .tpr file using that index. After running the command
gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o
prot_u3M_rerun -n water_urea_5ofprot.ndx
following error occur-
35099 atoms are not part of any of the T-Coupling groups
part of  .mdp file and index file is given below
rvdw=  1.2^M
fourierspacing = 0.12^M
fourier_nx = 0^M
fourier_ny = 0^M
fourier_nz = 0^M
pme_order = 4^M
ewald_rtol = 1e-5^M
optimize_fft = yes^M
; Berendsen temperature coupling is on in two groups^M
Tcoupl  =  V-rescale^M
tc-grps =  Protein   Urea_5ofprot^M
tau_t   =  0.10.1 ^M
ref_t   =  300300   ^M
; Energy monitoring^M
energygrps  =  Protein  Urea_5ofprot
; Isotropic pressure coupling is now on^M
Pcoupl  =  berendsen^M
  and at the end of the Index file i have only added the residue index of
urea within 5 of protein and save the index file.


While you can define whatever energygrps you like (note that the 
molecules will change over time and your results may end up being not 
useful), you need to couple all atoms in the system to a thermostat via 
tc-grps. Your urea selection is only a subset of the urea molecules, and 
if you have any other solvent, ions, etc. they are not being accounted 
for. tc-grps = Protein Non-Protein is almost always the way to go.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Re: [gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

[Quyen Vu]

>From your mdp file, I guess you did not couple solvent and ions.
How many atoms in your system? and how many for protein, how many for
Urea_5ofprot

On Tue, May 7, 2019 at 7:41 AM ISHRAT JAHAN  wrote:

> -- Forwarded message -
> From: ISHRAT JAHAN 
> Date: Tue, May 7, 2019 at 11:05 AM
> Subject: atoms are not part of any of the T-Coupling groups
> To: 
>
>
> Dear all,
> I am trying to calculate the lennard Jones interaction energy between
> protein and urea in the first solvation shell. I have made the index group
> of urea molecule in the first solvation shell and then tried to generate
> the .tpr file using that index. After running the command
> gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o
> prot_u3M_rerun -n water_urea_5ofprot.ndx
> following error occur-
> 35099 atoms are not part of any of the T-Coupling groups
> part of  .mdp file and index file is given below
> rvdw=  1.2^M
> fourierspacing = 0.12^M
> fourier_nx = 0^M
> fourier_ny = 0^M
> fourier_nz = 0^M
> pme_order = 4^M
> ewald_rtol = 1e-5^M
> optimize_fft = yes^M
> ; Berendsen temperature coupling is on in two groups^M
> Tcoupl  =  V-rescale^M
> tc-grps =  Protein   Urea_5ofprot^M
> tau_t   =  0.10.1 ^M
> ref_t   =  300300   ^M
> ; Energy monitoring^M
> energygrps  =  Protein  Urea_5ofprot
> ; Isotropic pressure coupling is now on^M
> Pcoupl  =  berendsen^M
>  and at the end of the Index file i have only added the residue index of
> urea within 5 of protein and save the index file.
>
> [ Urea_5ofprot ]
> 1261 1262 1263 1264 1265 1266 1267 1268 1301 1302 1303 1304 1305 1306 1307
> 1308 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362
> 1363 1364 1413 1414 1415 1416 1417 1418 1419 1420 1501 1502 1503 1504 1505
> 1506 1507 1508 1517 1518 1519 1520 1521 1522 1523 1524 1581 1582 1583 1584
> 1585 1586 1587 1588 1637 1638 1639 1640 1641 1642 1643 1644 1685 1686 1687
> 1688 1689 1690 1691 1692 1725 1726 1727 1728 1729 1730 1731 1732 1741 1742
> 1743 1744 1745 1746 1747 1748 1773 1774 1775 1776 1777 1778 1779 1780 1781
> 1782 1783 1784 1785 1786 1787 1788 1797 1798 1799 1800 1801 1802 1803 1804
> 1893 1894 1895 1896 1897 1898 1899 1900 1933 1934 1935 1936 1937 1938 1939
> 1940 1989 1990 1991 1992 1993 1994 1995 1996 2021 2022 2023 2024 2025 2026
> 2027 2028 2253 2254 2255 2256 2257 2258 2259 2260 2269 2270 2271 2272 2273
> 2274 2275 2276 2285 2286 2287 2288 2289 2290 2291 2292 2333 2334 2335 2336
> 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2365 2366 2367
> 2368 2369 2370 2371 2372 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502
> 2503 2504 2505 2506 2507 2508 2533 2534 2535 2536 2537 2538 2539 2540 2557
> 2558 2559 2560 2561 2562 2563 2564 2621 2622 2623 2624 2625 2626 2627 2628
> 2765 2766 2767 2768 2769 2770 2771 2772 2797 2798 2799 2800 2801 2802 2803
> 2804 2901 2902 2903 2904 2905 2906 2907 2908 2917 2918 2919 2920 2921 2922
> 2923 2924 2949 2950 2951 2952 2953 2954 2955 2956 3125 3126 3127 3128 3129
> 3130 3131 3132 3237 3238 3239 3240 3241 3242 3243 3244 3325 3326 3327 3328
> 3329 3330 3331 3332 3373 3374 3375 3376 3377 3378 3379 3380 3421 3422 3423
> 3424 3425 3426 3427 3428 3477 3478 3479 3480 3481 3482 3483 3484 3541 3542
> 3543 3544 3545 3546 3547 3548 3677 3678 3679 3680 3681 3682 3683 3684 3941
> 3942 3943 3944 3945 3946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956
> 3973 3974 3975 3976 3977 3978 3979 3980 4117 4118 4119 4120 4121 4122 4123
> 4124 4189 4190 4191 4192 4193 4194 4195 4196 4205 4206 4207 4208 4209 4210
> 4211 4212 4245 4246 4247 4248 4249 4250 4251 4252 4333 4334 4335 4336 4337
> 4338 4339 4340 4381 4382 4383 4384 4385 4386 4387 4388 4637 4638 4639 4640
> 4641 4642 4643 4644 4669 4670 4671 4672 4673 4674 4675 4676 4701 4702 4703
> 4704 4705 4706 4707 4708 4733 4734 4735 4736 4737 4738 4739 4740 4781 4782
> 4783 4784 4785 4786 4787 4788 4861 4862 4863 4864 4865 4866 4867 4868 4893
> 4894 4895 4896 4897 4898 4899 4900 4933 4934 4935 4936 4937 4938 4939 4940
> 5021 5022 5023 5024 5025 5026 5027 5028 5085 5086 5087 5088 5089 5090 5091
> 5092 5117 5118 5119 5120 5121 5122 5123 5124 5189 5190 5191 5192 5193 5194
> 5195 5196 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257
> 5258 5259 5260 5309 5310 5311 5312 5313 5314 5315 5316 5349 5350 5351 5352
> 5353 5354 5355 5356 5373 5374 5375 5376 5377 5378 5379 5380 5453 5454 5455
> 5456 5457 5458 5459 5460 5549 5550 5551 5552 5553 5554  5556 5565 5566
> 5567 5568 5569 5570 5571 5572 5581 5582 5583 5584 5585 5586 5587 5588 5669
> 5670 5671 5672 5673 5674 5675 5676 5693 5694 5695 5696 5697 5698 5699 5700
> 5813 5814 5815 5816 5817 5818 5819 5820 5901 5902 5903 5904 5905 5906 5907
> 5908 5949 5950 5951 5952 5953 5954 5955 5956 5973 5974 5975 5976 5977 5978
> 5979 5980 6005 6006 6007 6008 6009 6010 6011 6012 6061 6062 6063 6064 6065
> 6066 6067 6068 6253 6254 6255 6256 6257 

[gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

[ISHRAT JAHAN]

-- Forwarded message -
From: ISHRAT JAHAN 
Date: Tue, May 7, 2019 at 11:05 AM
Subject: atoms are not part of any of the T-Coupling groups
To: 


Dear all,
I am trying to calculate the lennard Jones interaction energy between
protein and urea in the first solvation shell. I have made the index group
of urea molecule in the first solvation shell and then tried to generate
the .tpr file using that index. After running the command
gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o
prot_u3M_rerun -n water_urea_5ofprot.ndx
following error occur-
35099 atoms are not part of any of the T-Coupling groups
part of  .mdp file and index file is given below
rvdw=  1.2^M
fourierspacing = 0.12^M
fourier_nx = 0^M
fourier_ny = 0^M
fourier_nz = 0^M
pme_order = 4^M
ewald_rtol = 1e-5^M
optimize_fft = yes^M
; Berendsen temperature coupling is on in two groups^M
Tcoupl  =  V-rescale^M
tc-grps =  Protein   Urea_5ofprot^M
tau_t   =  0.10.1 ^M
ref_t   =  300300   ^M
; Energy monitoring^M
energygrps  =  Protein  Urea_5ofprot
; Isotropic pressure coupling is now on^M
Pcoupl  =  berendsen^M
 and at the end of the Index file i have only added the residue index of
urea within 5 of protein and save the index file.

[ Urea_5ofprot ]
1261 1262 1263 1264 1265 1266 1267 1268 1301 1302 1303 1304 1305 1306 1307
1308 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362
1363 1364 1413 1414 1415 1416 1417 1418 1419 1420 1501 1502 1503 1504 1505
1506 1507 1508 1517 1518 1519 1520 1521 1522 1523 1524 1581 1582 1583 1584
1585 1586 1587 1588 1637 1638 1639 1640 1641 1642 1643 1644 1685 1686 1687
1688 1689 1690 1691 1692 1725 1726 1727 1728 1729 1730 1731 1732 1741 1742
1743 1744 1745 1746 1747 1748 1773 1774 1775 1776 1777 1778 1779 1780 1781
1782 1783 1784 1785 1786 1787 1788 1797 1798 1799 1800 1801 1802 1803 1804
1893 1894 1895 1896 1897 1898 1899 1900 1933 1934 1935 1936 1937 1938 1939
1940 1989 1990 1991 1992 1993 1994 1995 1996 2021 2022 2023 2024 2025 2026
2027 2028 2253 2254 2255 2256 2257 2258 2259 2260 2269 2270 2271 2272 2273
2274 2275 2276 2285 2286 2287 2288 2289 2290 2291 2292 2333 2334 2335 2336
2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2365 2366 2367
2368 2369 2370 2371 2372 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502
2503 2504 2505 2506 2507 2508 2533 2534 2535 2536 2537 2538 2539 2540 2557
2558 2559 2560 2561 2562 2563 2564 2621 2622 2623 2624 2625 2626 2627 2628
2765 2766 2767 2768 2769 2770 2771 2772 2797 2798 2799 2800 2801 2802 2803
2804 2901 2902 2903 2904 2905 2906 2907 2908 2917 2918 2919 2920 2921 2922
2923 2924 2949 2950 2951 2952 2953 2954 2955 2956 3125 3126 3127 3128 3129
3130 3131 3132 3237 3238 3239 3240 3241 3242 3243 3244 3325 3326 3327 3328
3329 3330 3331 3332 3373 3374 3375 3376 3377 3378 3379 3380 3421 3422 3423
3424 3425 3426 3427 3428 3477 3478 3479 3480 3481 3482 3483 3484 3541 3542
3543 3544 3545 3546 3547 3548 3677 3678 3679 3680 3681 3682 3683 3684 3941
3942 3943 3944 3945 3946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956
3973 3974 3975 3976 3977 3978 3979 3980 4117 4118 4119 4120 4121 4122 4123
4124 4189 4190 4191 4192 4193 4194 4195 4196 4205 4206 4207 4208 4209 4210
4211 4212 4245 4246 4247 4248 4249 4250 4251 4252 4333 4334 4335 4336 4337
4338 4339 4340 4381 4382 4383 4384 4385 4386 4387 4388 4637 4638 4639 4640
4641 4642 4643 4644 4669 4670 4671 4672 4673 4674 4675 4676 4701 4702 4703
4704 4705 4706 4707 4708 4733 4734 4735 4736 4737 4738 4739 4740 4781 4782
4783 4784 4785 4786 4787 4788 4861 4862 4863 4864 4865 4866 4867 4868 4893
4894 4895 4896 4897 4898 4899 4900 4933 4934 4935 4936 4937 4938 4939 4940
5021 5022 5023 5024 5025 5026 5027 5028 5085 5086 5087 5088 5089 5090 5091
5092 5117 5118 5119 5120 5121 5122 5123 5124 5189 5190 5191 5192 5193 5194
5195 5196 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257
5258 5259 5260 5309 5310 5311 5312 5313 5314 5315 5316 5349 5350 5351 5352
5353 5354 5355 5356 5373 5374 5375 5376 5377 5378 5379 5380 5453 5454 5455
5456 5457 5458 5459 5460 5549 5550 5551 5552 5553 5554  5556 5565 5566
5567 5568 5569 5570 5571 5572 5581 5582 5583 5584 5585 5586 5587 5588 5669
5670 5671 5672 5673 5674 5675 5676 5693 5694 5695 5696 5697 5698 5699 5700
5813 5814 5815 5816 5817 5818 5819 5820 5901 5902 5903 5904 5905 5906 5907
5908 5949 5950 5951 5952 5953 5954 5955 5956 5973 5974 5975 5976 5977 5978
5979 5980 6005 6006 6007 6008 6009 6010 6011 6012 6061 6062 6063 6064 6065
6066 6067 6068 6253 6254 6255 6256 6257 6258 6259 6260 6301 6302 6303 6304
6305 6306 6307 6308 6333 6334 6335 6336 6337 6338 6339 6340 6373 6374 6375
6376 6377 6378 6379 6380 6389 6390 6391 6392 6393 6394 6395 6396 6413 6414
6415 6416 6417 6418 6419 6420 6485 6486 6487 6488 6489 6490 6491 6492 6517
6518 6519 6520 6521 6522 6523 6524 6549 6550 6551 6552 6553 6554 6555 6556
6573 6574 6575 6576 6577 6578 

[gmx-users] Fwd: »Computational Electrophysiology«

[Harutyun Sahakyan]

Dear Gromacs users,

I am trying to simulate membrane potential using computational
electrophysiology protocol.

I modeled protein-membrane system with charmm-gui, equilibrate it and run
MD simulation. After some steps, I get this error.


===
starting mdrun 'Title'
5000 steps, 10.0 ps.
SWAP: Performed 35 swaps in step 100 for iontype POT.
SWAP: Performed 14 swaps in step 100 for iontype SOD.
step  200: timed with pme grid 72 72 108, coulomb cutoff 1.200: 2495.3
M-cycles

SWAP: Warning: 12 atoms were detected as being in both channels! Probably
your split
SWAP:  cylinder is way too large, or one compartment has collapsed
(step 200)
SWAP: Performed 1 swap in step 200 for iontype SOD.

SWAP: Warning: 8 atoms were detected as being in both channels! Probably
your split
SWAP:  cylinder is way too large, or one compartment has collapsed
(step 300)
SWAP: Performed 1 swap in step 300 for iontype POT.
SWAP: Performed 1 swap in step 300 for iontype SOD.
step  400: timed with pme grid 64 64 100, coulomb cutoff 1.327: 2610.4
M-cycles

SWAP: Warning: 8 atoms were detected as being in both channels! Probably
your split
SWAP:  cylinder is way too large, or one compartment has collapsed
(step 400)
SWAP: Performed 2 swaps in step 400 for iontype POT.
SWAP: Performed 2 swaps in step 400 for iontype SOD.

SWAP: Warning: 9 atoms were detected as being in both channels! Probably
your split
SWAP:  cylinder is way too large, or one compartment has collapsed
(step 500)
SWAP: Performed 1 swap in step 500 for iontype POT.
SWAP: Performed 2 swaps in step 500 for iontype SOD.
step  600: timed with pme grid 56 56 84, coulomb cutoff 1.538: 3583.0
M-cycles

SWAP: Warning: 8 atoms were detected as being in both channels! Probably
your split
SWAP:  cylinder is way too large, or one compartment has collapsed
(step 600)
SWAP: Performed 2 swaps in step 600 for iontype POT.
SWAP: Performed 1 swap in step 600 for iontype SOD.

SWAP: Warning: 6 atoms were detected as being in both channels! Probably
your split
SWAP:  cylinder is way too large, or one compartment has collapsed
(step 700)
SWAP: Performed 3 swaps in step 700 for iontype POT.

---
Program: gmx mdrun, version 2018.1
Source file: src/gromacs/swap/swapcoords.cpp (line 1911)

Fatal error:
Could not get index of SOL atom. Compartment contains 3 SOL molecules before
swaps.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
==



The number of steps before the error depends on ion concentrations in
compartments A and B. Moreover, the number of SOL molecules in the error
message can be different as well.

I have tried to change cylinder parameters however it does not solve the
problem.

Do you have any ideas? Have you faced this error before?

Channels are defined as several amino acids in the central parts of the
channel.

I attached my md.mdp file for more detailed information.



Thanks in advance.

Sincerely,

Harutyun Sahakyan

Senior assistant at Laboratory of

Computational Modeling of Biological Processes,

Institute of Molecular Biology, NAS, Armenia, Yerevan
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Re: [gmx-users] Fwd: Probability of number of atomic contacts

[Mahsa]

Hi,

When I use the tool, gmx analyze -dist, on the generated file from gmx
mindist for the number of contact, I can get the probability of number of
contacts. So I think if an appropriate index file and cut off distance are
defined by using this approach, I can get the probability of the first
shell coordination number for specific groups during the simulation time.
Is this correct? because the coordination number from gmx rdf gives the
average number of particles within a distance r.

Best regards,
Mahsa

On Fri, Mar 1, 2019 at 12:11 PM Mahsa  wrote:

> Hi Mark,
>
> Thank you for your reply! Actually, I should clarify my last post because
> it seems that I repeated my question :-)
> When I use the tool that Justin suggested, gmx analyze -dist, on the
> generated file from gmx mindist for the number of contact, I can get the
> probability of number of contacts. So I think if an appropriate index file
> and cut off distance are defined by using this approach, I can get the
> probability of the first shell coordination number for specific groups
> during the simulation time. Is this correct? because the coordination
> number from gmx rdf gives the average number of particles within a distance
> r.
>
> Best regards,
> Mahsa
>
> On Fri, Mar 1, 2019 at 5:04 AM Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Which GROMACS tools documentation did you check to see whether it can be
>> done already? :-) I don't know the answer, but that's where to start!
>>
>> Mark
>>
>> On Thu., 28 Feb. 2019, 10:43 Mahsa,  wrote:
>>
>> > Thank you very much for your comments!
>> >
>> > How would it be possible to get probability vs. number of contacts or
>> > probability vs coordination number averaged across the simulations? Can
>> it
>> > be done directly with Gromacs tools or I need some scripts for that?
>> >
>> > Best regards,
>> > Mahsa
>> >
>> > On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul  wrote:
>> >
>> > >
>> > >
>> > > On 2/28/19 8:59 AM, Mahsa wrote:
>> > > > Hi Justin,
>> > > >
>> > > > Could you please comment on my questions in the previous post?
>> > > >
>> > > > Best regards,
>> > > > Mahsa
>> > > >
>> > > > -- Forwarded message -
>> > > > From: Mahsa 
>> > > > Date: Sun, Feb 17, 2019 at 2:36 PM
>> > > > Subject: Re: [gmx-users] Probability of number of atomic contacts
>> > > > To: 
>> > > >
>> > > >
>> > > > Thank you very much, Justin!
>> > > >
>> > > > I tried this command:
>> > > >
>> > > > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg
>> > > >
>> > > >
>> > > > and I got a histogram. Now the number of contacts between the ion
>> and
>> > the
>> > > > polymer is between 160-180. I just want to be sure if I am doing
>> this
>> > > > analysis correct. When I use gmx mindist, from the index file I
>> choose
>> > a
>> > > > group of the ion (including 46 ions) and then the polymer group (all
>> > > > polymer chains in the box).  I think maybe instead of choosing all
>> > ions,
>> > > I
>> > > > should only select one of them and get the number of contact with
>> the
>> > > > polymers but then since I have 46 of this ion in the simulation box,
>> > can
>> > > it
>> > > > be a good representative of the whole system? If not, what else can
>> I
>> > do
>> > > in
>> > > > this case?
>> > >
>> > > I don't see any point in doing per-ion analysis. You already have the
>> > > answer you want with respect to contacts between the two species.
>> > > Choosing one ion isn't necessarily going to be representative, either.
>> > >
>> > > > Besides, it is mentioned in the Gromacs manual, that if we use the
>> > > > -group option
>> > > > a contact of an atom in another group with multiple atoms in the
>> first
>> > > > group is counted as one contact instead of as multiple contacts. I
>> want
>> > > to
>> > > > count all contact with a polymer chain as 1 contact and check the
>> > number
>> > > of
>> > > > contacts with different polymer chains so by using -group and having
>> > the
>> > > > ion as the first group and polymer as the second group from the
>> index
>> > > file,
>> > > > can I get this?
>> > >
>> > > This option is primarily used to avoid over-counting, e.g. the
>> > > interaction between an ion and carboxylate oxygens will not be counted
>> > > as two contact if each ion-oxygen distance satisfies the criterion;
>> it's
>> > > just one.
>> > >
>> > > > The last question, can I do the same approach to get the
>> distribution
>> > of
>> > > > coordination number for the first coordination shell of ions and
>> > special
>> > > > atoms of the polymers?
>> > >
>> > > You can calculate coordination number by integrating an RDF.
>> > >
>> > > -Justin
>> > >
>> > > --
>> > > ==
>> > >
>> > > Justin A. Lemkul, Ph.D.
>> > > Assistant Professor
>> > > Office: 301 Fralin Hall
>> > > Lab: 303 Engel Hall
>> > >
>> > > Virginia Tech Department of Biochemistry
>> > > 340 West Campus Dr.
>> > > Blacksburg, VA 24061
>> > >
>> > > jalem...@vt.edu | (540) 231-3129
>> > > 

[gmx-users] Fwd: Data collection xtc file

[Alex]

Any idea please?
Thanks.
Alex

-- Forwarded message -
From: Alex 
Date: Tue, Mar 5, 2019 at 1:10 PM
Subject: Data collection xtc file
To: 


Dear all,
Here is the data collection part of a simulation's mdp file:

integrator   = md
dt   = 0.002 ; 2 fs
nsteps   = 5000   ; 100 ns
xtc-precision= 1000
nstlist  = 40

;;in .trr file
nstxout  = 1
nstvout  = 1000
nstfout  = 0
;;in energy file.log
nstlog   = 200
nstcalcenergy= 10
nstenergy= 200
;;in xtc file
nstxout-compressed   = 50

The simulation is running and now is in  38753000 step (77506 ns time).
Using the gmx_mpi trjconv I am trying to dump out some frames from the .xtc
file at times t= 71000 ns, t= 75000 ns and t= 76000 ns, however, the
outputs gro files are surprisingly empty. The Precision of out.xtc is 0.001
(nm) and it said that "WARNING no output, last frame read at t=70352.3".
Considering the parameters above I wonder if it is reasonable to have no
stored  frame after t=70352.3 to t= 76000 ns?

The Gromacs version is 18.6.

Regards,
Alex
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Re: [gmx-users] Fwd: Probability of number of atomic contacts

[Mahsa]

Hi Mark,

Thank you for your reply! Actually, I should clarify my last post because
it seems that I repeated my question :-)
When I use the tool that Justin suggested, gmx analyze -dist, on the
generated file from gmx mindist for the number of contact, I can get the
probability of number of contacts. So I think if an appropriate index file
and cut off distance are defined by using this approach, I can get the
probability of the first shell coordination number for specific groups
during the simulation time. Is this correct? because the coordination
number from gmx rdf gives the average number of particles within a distance
r.

Best regards,
Mahsa

On Fri, Mar 1, 2019 at 5:04 AM Mark Abraham 
wrote:

> Hi,
>
> Which GROMACS tools documentation did you check to see whether it can be
> done already? :-) I don't know the answer, but that's where to start!
>
> Mark
>
> On Thu., 28 Feb. 2019, 10:43 Mahsa,  wrote:
>
> > Thank you very much for your comments!
> >
> > How would it be possible to get probability vs. number of contacts or
> > probability vs coordination number averaged across the simulations? Can
> it
> > be done directly with Gromacs tools or I need some scripts for that?
> >
> > Best regards,
> > Mahsa
> >
> > On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 2/28/19 8:59 AM, Mahsa wrote:
> > > > Hi Justin,
> > > >
> > > > Could you please comment on my questions in the previous post?
> > > >
> > > > Best regards,
> > > > Mahsa
> > > >
> > > > -- Forwarded message -
> > > > From: Mahsa 
> > > > Date: Sun, Feb 17, 2019 at 2:36 PM
> > > > Subject: Re: [gmx-users] Probability of number of atomic contacts
> > > > To: 
> > > >
> > > >
> > > > Thank you very much, Justin!
> > > >
> > > > I tried this command:
> > > >
> > > > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg
> > > >
> > > >
> > > > and I got a histogram. Now the number of contacts between the ion and
> > the
> > > > polymer is between 160-180. I just want to be sure if I am doing this
> > > > analysis correct. When I use gmx mindist, from the index file I
> choose
> > a
> > > > group of the ion (including 46 ions) and then the polymer group (all
> > > > polymer chains in the box).  I think maybe instead of choosing all
> > ions,
> > > I
> > > > should only select one of them and get the number of contact with the
> > > > polymers but then since I have 46 of this ion in the simulation box,
> > can
> > > it
> > > > be a good representative of the whole system? If not, what else can I
> > do
> > > in
> > > > this case?
> > >
> > > I don't see any point in doing per-ion analysis. You already have the
> > > answer you want with respect to contacts between the two species.
> > > Choosing one ion isn't necessarily going to be representative, either.
> > >
> > > > Besides, it is mentioned in the Gromacs manual, that if we use the
> > > > -group option
> > > > a contact of an atom in another group with multiple atoms in the
> first
> > > > group is counted as one contact instead of as multiple contacts. I
> want
> > > to
> > > > count all contact with a polymer chain as 1 contact and check the
> > number
> > > of
> > > > contacts with different polymer chains so by using -group and having
> > the
> > > > ion as the first group and polymer as the second group from the index
> > > file,
> > > > can I get this?
> > >
> > > This option is primarily used to avoid over-counting, e.g. the
> > > interaction between an ion and carboxylate oxygens will not be counted
> > > as two contact if each ion-oxygen distance satisfies the criterion;
> it's
> > > just one.
> > >
> > > > The last question, can I do the same approach to get the distribution
> > of
> > > > coordination number for the first coordination shell of ions and
> > special
> > > > atoms of the polymers?
> > >
> > > You can calculate coordination number by integrating an RDF.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Office: 301 Fralin Hall
> > > Lab: 303 Engel Hall
> > >
> > > Virginia Tech Department of Biochemistry
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalem...@vt.edu | (540) 231-3129
> > > http://www.thelemkullab.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
> > >
> > > * 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 

Re: [gmx-users] Fwd: Probability of number of atomic contacts

[Mark Abraham]

Hi,

Which GROMACS tools documentation did you check to see whether it can be
done already? :-) I don't know the answer, but that's where to start!

Mark

On Thu., 28 Feb. 2019, 10:43 Mahsa,  wrote:

> Thank you very much for your comments!
>
> How would it be possible to get probability vs. number of contacts or
> probability vs coordination number averaged across the simulations? Can it
> be done directly with Gromacs tools or I need some scripts for that?
>
> Best regards,
> Mahsa
>
> On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul  wrote:
>
> >
> >
> > On 2/28/19 8:59 AM, Mahsa wrote:
> > > Hi Justin,
> > >
> > > Could you please comment on my questions in the previous post?
> > >
> > > Best regards,
> > > Mahsa
> > >
> > > -- Forwarded message -
> > > From: Mahsa 
> > > Date: Sun, Feb 17, 2019 at 2:36 PM
> > > Subject: Re: [gmx-users] Probability of number of atomic contacts
> > > To: 
> > >
> > >
> > > Thank you very much, Justin!
> > >
> > > I tried this command:
> > >
> > > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg
> > >
> > >
> > > and I got a histogram. Now the number of contacts between the ion and
> the
> > > polymer is between 160-180. I just want to be sure if I am doing this
> > > analysis correct. When I use gmx mindist, from the index file I choose
> a
> > > group of the ion (including 46 ions) and then the polymer group (all
> > > polymer chains in the box).  I think maybe instead of choosing all
> ions,
> > I
> > > should only select one of them and get the number of contact with the
> > > polymers but then since I have 46 of this ion in the simulation box,
> can
> > it
> > > be a good representative of the whole system? If not, what else can I
> do
> > in
> > > this case?
> >
> > I don't see any point in doing per-ion analysis. You already have the
> > answer you want with respect to contacts between the two species.
> > Choosing one ion isn't necessarily going to be representative, either.
> >
> > > Besides, it is mentioned in the Gromacs manual, that if we use the
> > > -group option
> > > a contact of an atom in another group with multiple atoms in the first
> > > group is counted as one contact instead of as multiple contacts. I want
> > to
> > > count all contact with a polymer chain as 1 contact and check the
> number
> > of
> > > contacts with different polymer chains so by using -group and having
> the
> > > ion as the first group and polymer as the second group from the index
> > file,
> > > can I get this?
> >
> > This option is primarily used to avoid over-counting, e.g. the
> > interaction between an ion and carboxylate oxygens will not be counted
> > as two contact if each ion-oxygen distance satisfies the criterion; it's
> > just one.
> >
> > > The last question, can I do the same approach to get the distribution
> of
> > > coordination number for the first coordination shell of ions and
> special
> > > atoms of the polymers?
> >
> > You can calculate coordination number by integrating an RDF.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.thelemkullab.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
> >
> > * 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!
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Re: [gmx-users] Fwd: Probability of number of atomic contacts

[Mahsa]

Thank you very much for your comments!

How would it be possible to get probability vs. number of contacts or
probability vs coordination number averaged across the simulations? Can it
be done directly with Gromacs tools or I need some scripts for that?

Best regards,
Mahsa

On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul  wrote:

>
>
> On 2/28/19 8:59 AM, Mahsa wrote:
> > Hi Justin,
> >
> > Could you please comment on my questions in the previous post?
> >
> > Best regards,
> > Mahsa
> >
> > -- Forwarded message -
> > From: Mahsa 
> > Date: Sun, Feb 17, 2019 at 2:36 PM
> > Subject: Re: [gmx-users] Probability of number of atomic contacts
> > To: 
> >
> >
> > Thank you very much, Justin!
> >
> > I tried this command:
> >
> > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg
> >
> >
> > and I got a histogram. Now the number of contacts between the ion and the
> > polymer is between 160-180. I just want to be sure if I am doing this
> > analysis correct. When I use gmx mindist, from the index file I choose a
> > group of the ion (including 46 ions) and then the polymer group (all
> > polymer chains in the box).  I think maybe instead of choosing all ions,
> I
> > should only select one of them and get the number of contact with the
> > polymers but then since I have 46 of this ion in the simulation box, can
> it
> > be a good representative of the whole system? If not, what else can I do
> in
> > this case?
>
> I don't see any point in doing per-ion analysis. You already have the
> answer you want with respect to contacts between the two species.
> Choosing one ion isn't necessarily going to be representative, either.
>
> > Besides, it is mentioned in the Gromacs manual, that if we use the
> > -group option
> > a contact of an atom in another group with multiple atoms in the first
> > group is counted as one contact instead of as multiple contacts. I want
> to
> > count all contact with a polymer chain as 1 contact and check the number
> of
> > contacts with different polymer chains so by using -group and having the
> > ion as the first group and polymer as the second group from the index
> file,
> > can I get this?
>
> This option is primarily used to avoid over-counting, e.g. the
> interaction between an ion and carboxylate oxygens will not be counted
> as two contact if each ion-oxygen distance satisfies the criterion; it's
> just one.
>
> > The last question, can I do the same approach to get the distribution of
> > coordination number for the first coordination shell of ions and special
> > atoms of the polymers?
>
> You can calculate coordination number by integrating an RDF.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.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
>
> * 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] Fwd: Probability of number of atomic contacts

[Justin Lemkul]

On 2/28/19 8:59 AM, Mahsa wrote:

Hi Justin,

Could you please comment on my questions in the previous post?

Best regards,
Mahsa

-- Forwarded message -
From: Mahsa 
Date: Sun, Feb 17, 2019 at 2:36 PM
Subject: Re: [gmx-users] Probability of number of atomic contacts
To: 


Thank you very much, Justin!

I tried this command:

gmx_seq analyze -f numcont.xvg -dist num_dist.xvg


and I got a histogram. Now the number of contacts between the ion and the
polymer is between 160-180. I just want to be sure if I am doing this
analysis correct. When I use gmx mindist, from the index file I choose a
group of the ion (including 46 ions) and then the polymer group (all
polymer chains in the box).  I think maybe instead of choosing all ions, I
should only select one of them and get the number of contact with the
polymers but then since I have 46 of this ion in the simulation box, can it
be a good representative of the whole system? If not, what else can I do in
this case?


I don't see any point in doing per-ion analysis. You already have the 
answer you want with respect to contacts between the two species. 
Choosing one ion isn't necessarily going to be representative, either.



Besides, it is mentioned in the Gromacs manual, that if we use the
-group option
a contact of an atom in another group with multiple atoms in the first
group is counted as one contact instead of as multiple contacts. I want to
count all contact with a polymer chain as 1 contact and check the number of
contacts with different polymer chains so by using -group and having the
ion as the first group and polymer as the second group from the index file,
can I get this?


This option is primarily used to avoid over-counting, e.g. the 
interaction between an ion and carboxylate oxygens will not be counted 
as two contact if each ion-oxygen distance satisfies the criterion; it's 
just one.



The last question, can I do the same approach to get the distribution of
coordination number for the first coordination shell of ions and special
atoms of the polymers?


You can calculate coordination number by integrating an RDF.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

--
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[gmx-users] Fwd: Probability of number of atomic contacts

[Mahsa]

Hi Justin,

Could you please comment on my questions in the previous post?

Best regards,
Mahsa

-- Forwarded message -
From: Mahsa 
Date: Sun, Feb 17, 2019 at 2:36 PM
Subject: Re: [gmx-users] Probability of number of atomic contacts
To: 


Thank you very much, Justin!

I tried this command:

gmx_seq analyze -f numcont.xvg -dist num_dist.xvg


and I got a histogram. Now the number of contacts between the ion and the
polymer is between 160-180. I just want to be sure if I am doing this
analysis correct. When I use gmx mindist, from the index file I choose a
group of the ion (including 46 ions) and then the polymer group (all
polymer chains in the box).  I think maybe instead of choosing all ions, I
should only select one of them and get the number of contact with the
polymers but then since I have 46 of this ion in the simulation box, can it
be a good representative of the whole system? If not, what else can I do in
this case?

Besides, it is mentioned in the Gromacs manual, that if we use the
-group option
a contact of an atom in another group with multiple atoms in the first
group is counted as one contact instead of as multiple contacts. I want to
count all contact with a polymer chain as 1 contact and check the number of
contacts with different polymer chains so by using -group and having the
ion as the first group and polymer as the second group from the index file,
can I get this?

The last question, can I do the same approach to get the distribution of
coordination number for the first coordination shell of ions and special
atoms of the polymers?

Best regards,
Mahsa

On Sun, Feb 17, 2019 at 1:39 PM Justin Lemkul  wrote:

>
>
> On 2/17/19 7:21 AM, Mahsa wrote:
> > Dear Gromacs users,
> >
> > I want to get histograms of the number of polymer-ion contacts average
> > across the simulation. For this I used,
> >
> > gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od
> mindist.xvg
> > -on numcont.xvg -or mindistres.xvg -group
> >
> > and from the index file, I chose the ion first and then the polymer
> group.
> > The generated file numcont.xvg which is more related to what I am looking
> > for, gives number of contacts vs time. How can I get the information
> which
> > I look for from this analysis?
>
> Post-process with gmx analyze -dist
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.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
>
> * 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] Fwd: Maximum number density in gmx densmap

[Alex]

Dear all,
Any idea on my questions, please?

Mostafa;
Using gmx densmap first produce a .xpm file;
~> gmx densmap -f case.xtc -s case.tpr -n index.ndx -o case.xpm -unit nm-3
-bin 0.02
The case.xpm file is a matrix, one way provided by Gromacs to visualize a
matrix is to convert it to a eps file for instance, you can do that using
gmx xmp2ps;
~> gmx xpm2ps -f case.xpm -di m2p.m2p -o case.eps -bx 2 -by 2 -rainbow blue

Thank you
Alex

On Tue, Feb 12, 2019 at 2:19 PM Mostafa Fakhraee <
fakhraee.mosta...@gmail.com> wrote:

> Dear Alex
>
> Is it possible to send the command you have used for extracting 2D densmap?
>
>
>
> On Tue, Feb 12, 2019 at 10:39 PM Alex  wrote:
>
> > Dear all,
> > Following my last email, I also calculated the 2D density number for
> water
> > molecules for the same system, as you can see in the link below the
> maximum
> > water number density interestingly is 120 nm^-3 for the region with the
> > bulk water whose the number density should be around 33.36 nm^-3. The box
> > size of my system is ``7.552, 7.552, 7.552" and the bin grid size was
> > chosen to be 0.01 nm.
> > I tried to make a connection between the 120 nm^-3 given for the bulk
> water
> > region by the gmx densmap and reall water number density of 33.36 nm^-3 .
> > Considering the above box information I would be so appreciated if one
> > could explain what I am doing wrong?
> >
> > https://drive.google.com/open?id=1HvSnUahNklTONmthYPXdCwB8g2kzRXVe
> >
> > Thank you
> > Alex
> >
> > -- Forwarded message -
> > From: Alex 
> > Date: Tue, Feb 12, 2019 at 5:20 AM
> > Subject: Maximum number density in gmx densmap
> > To: gmx-us...@gromacs.org 
> >
> >
> > Dear all,
> > Using the gmx densmap I have calculated the 2D density number in x-y
> plain
> > for a droplet containing 58 molecules. With nm^-3 (nm^-2) as unit the
> > maximum number density turn out to be 97.83 (738.38). I wonder what
> exactly
> > has been counted here as the representative of each molecules? Is it for
> > instance the center of mass of each molecule?
> > And is the gmx densmap exactly the gmx density but in two dimensions?
> >
> > Thank you,
> > Regards
> > Alex
> > --
> > 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.
> >
>
>
> --
>  
>  Best Regards,
>  Mostafa Fakhraee
>  ===
>  PhD Student of Physical Chemistry,
>  Department of Chemistry,
>  Sharif University of Technology, Tehran, Iran.
>  Official Email: mostafa_fakhr...@ch.sharif.ir  >
>  Email: mostafa.fakhr...@yahoo.com
>   ===
> --
> 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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>
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>
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Re: [gmx-users] Fwd: Maximum number density in gmx densmap

[Mostafa Fakhraee]

Dear Alex

Is it possible to send the command you have used for extracting 2D densmap?



On Tue, Feb 12, 2019 at 10:39 PM Alex  wrote:

> Dear all,
> Following my last email, I also calculated the 2D density number for water
> molecules for the same system, as you can see in the link below the maximum
> water number density interestingly is 120 nm^-3 for the region with the
> bulk water whose the number density should be around 33.36 nm^-3. The box
> size of my system is ``7.552, 7.552, 7.552" and the bin grid size was
> chosen to be 0.01 nm.
> I tried to make a connection between the 120 nm^-3 given for the bulk water
> region by the gmx densmap and reall water number density of 33.36 nm^-3 .
> Considering the above box information I would be so appreciated if one
> could explain what I am doing wrong?
>
> https://drive.google.com/open?id=1HvSnUahNklTONmthYPXdCwB8g2kzRXVe
>
> Thank you
> Alex
>
> -- Forwarded message -
> From: Alex 
> Date: Tue, Feb 12, 2019 at 5:20 AM
> Subject: Maximum number density in gmx densmap
> To: gmx-us...@gromacs.org 
>
>
> Dear all,
> Using the gmx densmap I have calculated the 2D density number in x-y plain
> for a droplet containing 58 molecules. With nm^-3 (nm^-2) as unit the
> maximum number density turn out to be 97.83 (738.38). I wonder what exactly
> has been counted here as the representative of each molecules? Is it for
> instance the center of mass of each molecule?
> And is the gmx densmap exactly the gmx density but in two dimensions?
>
> Thank you,
> Regards
> Alex
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>


-- 
 
 Best Regards,
 Mostafa Fakhraee
 ===
 PhD Student of Physical Chemistry,
 Department of Chemistry,
 Sharif University of Technology, Tehran, Iran.
 Official Email: mostafa_fakhr...@ch.sharif.ir 
 Email: mostafa.fakhr...@yahoo.com
  ===
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[gmx-users] Fwd: Maximum number density in gmx densmap

[Alex]

Dear all,
Following my last email, I also calculated the 2D density number for water
molecules for the same system, as you can see in the link below the maximum
water number density interestingly is 120 nm^-3 for the region with the
bulk water whose the number density should be around 33.36 nm^-3. The box
size of my system is ``7.552, 7.552, 7.552" and the bin grid size was
chosen to be 0.01 nm.
I tried to make a connection between the 120 nm^-3 given for the bulk water
region by the gmx densmap and reall water number density of 33.36 nm^-3 .
Considering the above box information I would be so appreciated if one
could explain what I am doing wrong?

https://drive.google.com/open?id=1HvSnUahNklTONmthYPXdCwB8g2kzRXVe

Thank you
Alex

-- Forwarded message -
From: Alex 
Date: Tue, Feb 12, 2019 at 5:20 AM
Subject: Maximum number density in gmx densmap
To: gmx-us...@gromacs.org 


Dear all,
Using the gmx densmap I have calculated the 2D density number in x-y plain
for a droplet containing 58 molecules. With nm^-3 (nm^-2) as unit the
maximum number density turn out to be 97.83 (738.38). I wonder what exactly
has been counted here as the representative of each molecules? Is it for
instance the center of mass of each molecule?
And is the gmx densmap exactly the gmx density but in two dimensions?

Thank you,
Regards
Alex
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Re: [gmx-users] Fwd: Phosphorylated serine and threonine residues (Gromacs MD)

[Najamuddin Memon]

Dear use 43a1 extended phosphorylated force field. Although phosphorylated
amino acids are not in the active site or not involved in the interaction
with ligand but in broad context these phosphorylated residues have impact
on structure of protein over the function of time


On Mon, Feb 11, 2019, 6:32 PM Swapnil Bhujbal  Dear all,
>
> I am working with a protein having phosphorylated serine and threonine
> residues. I will be performing ligand-protein MD. These phosphorylated
> amino acid residues are not located in the active site of protein.
> Should I just replace the phosphorylated serine and threonine residues with
> serine and threonine before MD preparations? Or shoild I ignore them
> because they will not be involved in any interactions with the ligand? Or
> do we have different force fields for the phosphorylated residues ?
>
> Your suggestions are highly appreciated.
>
> Thank you.
>
> Sincerely,
> Mr. Swapnil Bhujbal
> PhD Scholar,
> School of Medicine,
> Chosun University,
> South Korea.
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[gmx-users] Fwd: Phosphorylated serine and threonine residues (Gromacs MD)

[Swapnil Bhujbal]

Dear all,

I am working with a protein having phosphorylated serine and threonine
residues. I will be performing ligand-protein MD. These phosphorylated
amino acid residues are not located in the active site of protein.
Should I just replace the phosphorylated serine and threonine residues with
serine and threonine before MD preparations? Or shoild I ignore them
because they will not be involved in any interactions with the ligand? Or
do we have different force fields for the phosphorylated residues ?

Your suggestions are highly appreciated.

Thank you.

Sincerely,
Mr. Swapnil Bhujbal
PhD Scholar,
School of Medicine,
Chosun University,
South Korea.
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[gmx-users] Fwd: Query regarding Preferential Interaction Coefficient Calculation

[ISHRAT JAHAN]

Dear all,
I want to calculate the number of water and osmolyte molecule at particular
distance from surface of protein in order to calculate preferential
interaction coefficient. I had calculated it using gmx select command. Is
it right to calculate using this command. Please help me in this regard.
Thanks in advance

-- Forwarded message -
From: ISHRAT JAHAN 
Date: Wed, Jan 16, 2019, 11:23 AM
Subject: Query regarding Preferential Interaction Coefficient Calculation
To: 


Dear all,
I have done the MD simulation of protein in osmolytes, now i want to
calculate the preferential interaction coefficient of osmolytes from
protein surface.Will anyone please guide me the proper steps of the
calculation?
Thanks and regards
-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh
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[gmx-users] Fwd:

[Soham Sarkar]

Dear all,
This is the error I get while executing the grompp command
 " Program grompp, VERSION 4.5.6
Source code file: topio.c, line: 582
Fatal error:
Syntax error - File tris.itp, line 19
Last line read:
' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT "
I gave the command like:
" grompp -f ions.mdp -c solv.gro -o ions.tpr -p system.top
 "
I am attaching the input files. I have generated the tris.itp from tppmktop
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Re: [gmx-users] Fwd: Mismatch between gromacs and python-networkx versions

[Justin Lemkul]

On 11/26/18 12:54 PM, Francesco Pietra wrote:

Hurrying - as with my post above - is seldom a good procedure.
The next step, converting ligand_ini.pdb to ligand.gro did not work well,
i.e., for GDP the .gro file reads
S  C  A  M  O  R  G
40
 0/scrPB1   0.100   0.000   0.100
 0/scr   O1B2   0.100   0.000   0.100
 0/scr   O2B3   0.100   0.000   0.100
 0/scr   O3B4   0.100   0.000   0.100
 0/scr   O3A5   0.100   0.000   0.100
 0/scrPA6   0.100   0.000   0.100

which came anyway unespected as the ligand_ini.pdb looks like to be correct

ATOM  1 PB   /scratch/phpK1JFey_GDP_H.pdb1 320.960 448.853
308.012  1.00  0.00
ATOM  2 O1B  /scratch/phpK1JFey_GDP_H.pdb1 320.256 449.824
307.091  1.00  0.00
ATOM  3 O2B  /scratch/phpK1JFey_GDP_H.pdb1 320.922 447.397
307.609  1.00  0.00
ATOM  4 O3B  /scratch/phpK1JFey_GDP_H.pdb1 320.622 449.126
309.460  1.00  0.00
ATOM  5 O3A  /scratch/phpK1JFey_GDP_H.pdb1 322.508 449.269
307.860  1.00  0.00
ATOM  6 PA   /scratch/phpK1JFey_GDP_H.pdb1 323.692 448.599
308.726  1.00  0.00
ATOM  7 O1A  /scratch/phpK1JFey_GDP_H.pdb1 324.384 447.624
307.801  1.00  0.00 came unexpected, as the ligand_ini.pdb looks like to be
correct


You need a sensible name in your @TRIPOS definition, with no 
more than 4 characters. Your file has the name of a full path to a file 
in it.


-Justin


fp

-- Forwarded message -
From: Francesco Pietra 
Date: Mon, Nov 26, 2018 at 6:25 PM
Subject: Re: [gmx-users] Mismatch between gromacs and python-networkx
versions
To: 


This is to let you know, that the fixed .mol2 (got by first removing #
comments, as you indicated), the script cgenff_charmm2gmx.py works well
with the NetworkX 2x and charmm36-nov2018.ff. I still have to run gromacs
with them, but the content of the files looks like to be what was expected.
fp

thanks again

On Mon, Nov 26, 2018 at 3:57 PM Justin Lemkul  wrote:



On 11/25/18 9:10 AM, Francesco Pietra wrote:

This is my first post to gromacs, to which I came in the hope that FEP
simulations are more efficient than with other engines.

I updated debian amd64 from stretch to buster in order to have the said
preferred gromacs 2018 (2016 on stretch). Now, to set up the system
(protein+ligands) I have networkx2.x, while 1.11.x (which was on stretch)
is required. Am I wrong, or there is really such a mismatch?. If so, how

to

turn around? I have only one version of linux.

GROMACS has no NetworkX requirement. If you're talking about the
cgenff_charmm2gmx.py script, that's different. You need NetworkX 1.11
for it to work. But that's not a GROMACS issue.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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[gmx-users] Fwd: Mismatch between gromacs and python-networkx versions

[Francesco Pietra]

Hurrying - as with my post above - is seldom a good procedure.
The next step, converting ligand_ini.pdb to ligand.gro did not work well,
i.e., for GDP the .gro file reads
S  C  A  M  O  R  G
   40
0/scrPB1   0.100   0.000   0.100
0/scr   O1B2   0.100   0.000   0.100
0/scr   O2B3   0.100   0.000   0.100
0/scr   O3B4   0.100   0.000   0.100
0/scr   O3A5   0.100   0.000   0.100
0/scrPA6   0.100   0.000   0.100

which came anyway unespected as the ligand_ini.pdb looks like to be correct

ATOM  1 PB   /scratch/phpK1JFey_GDP_H.pdb1 320.960 448.853
308.012  1.00  0.00
ATOM  2 O1B  /scratch/phpK1JFey_GDP_H.pdb1 320.256 449.824
307.091  1.00  0.00
ATOM  3 O2B  /scratch/phpK1JFey_GDP_H.pdb1 320.922 447.397
307.609  1.00  0.00
ATOM  4 O3B  /scratch/phpK1JFey_GDP_H.pdb1 320.622 449.126
309.460  1.00  0.00
ATOM  5 O3A  /scratch/phpK1JFey_GDP_H.pdb1 322.508 449.269
307.860  1.00  0.00
ATOM  6 PA   /scratch/phpK1JFey_GDP_H.pdb1 323.692 448.599
308.726  1.00  0.00
ATOM  7 O1A  /scratch/phpK1JFey_GDP_H.pdb1 324.384 447.624
307.801  1.00  0.00 came unexpected, as the ligand_ini.pdb looks like to be
correct

fp

-- Forwarded message -
From: Francesco Pietra 
Date: Mon, Nov 26, 2018 at 6:25 PM
Subject: Re: [gmx-users] Mismatch between gromacs and python-networkx
versions
To: 


This is to let you know, that the fixed .mol2 (got by first removing #
comments, as you indicated), the script cgenff_charmm2gmx.py works well
with the NetworkX 2x and charmm36-nov2018.ff. I still have to run gromacs
with them, but the content of the files looks like to be what was expected.
fp

thanks again

On Mon, Nov 26, 2018 at 3:57 PM Justin Lemkul  wrote:

>
>
> On 11/25/18 9:10 AM, Francesco Pietra wrote:
> > This is my first post to gromacs, to which I came in the hope that FEP
> > simulations are more efficient than with other engines.
> >
> > I updated debian amd64 from stretch to buster in order to have the said
> > preferred gromacs 2018 (2016 on stretch). Now, to set up the system
> > (protein+ligands) I have networkx2.x, while 1.11.x (which was on stretch)
> > is required. Am I wrong, or there is really such a mismatch?. If so, how
> to
> > turn around? I have only one version of linux.
>
> GROMACS has no NetworkX requirement. If you're talking about the
> cgenff_charmm2gmx.py script, that's different. You need NetworkX 1.11
> for it to work. But that's not a GROMACS issue.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
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[gmx-users] Fwd: Gromacs 2018.3 with CUDA - segmentation fault (core dumped)

[Krzysztof Kolman]

>
>
> Dear Benson and Szilard,
>
> Thank you for your interest. Benson, I will try to answer you questions
> first:
> 1) No, I have only tested 2018.3 so far. I just changed from Gromacs 5.1.4
> and these are my first tests.
> 2) Not yet but I plan to do it.
> 3) The results look reasonable after restart
> 4) I think so but I did not this time. My computer has 16 gb of ram and I
> checked the ram utilization 2h before the crash. It was only using 2gb out
> of 16gb.
> 5) I use my private computer so I think it should be possible to recompile
> if needed or run with debug infortmation.
>
> Szilard. No but they are quite close. The first crashed happened at
> 22536600, the second one 45006200. I did earlier different simulation
> and it also crashed (seg fault) after around 12 h.
>

   Ok. After more research I have manage to solve the problem. Mdrun with
following flags does not trigger seg fault anymore:
   gmx mdrun -v -deffnm md_0_1 -nb gpu -pme cpu -pmefft cpu



> Best regards,
> Krzysztof
>
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[gmx-users] Fwd: thread_GROMACs_question

[Dallas Warren]

First off, you should keep this on the emailing list.  I have included the
emailing list in the reply.  No need to take it to private email.

Did you read the link that I sent with the reply?  You even have the
simulation box visualised with the vmd screen shot you sent, so that should
be a big clue to you what is going on.  Have a play with the vmd periodic
images tab, it should very quickly make sense.

From what gmx distance says, I don't think you need to use any pbc
processing before doing the calculations, it takes pbc into consideration.
The processing you did has probably messed things up, most likely the
nojump.  And the graphs indicate this fact too.

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, 24 Oct 2018 at 09:32, Antonio Carlesso 
wrote:

> Dear Warren,
>
> I am a PhD student at the University of Göteborg (Sweden).
>
>
> Since you should be an MD expert I would like to ask you one more stuff
> regarding this thread (hope I will not bother you):
>
>
> https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg34909.html
>
>
>
>
>
>
>
>
>
> Do you have any reason why  calculating the distance over time between
> two pair of atoms (Oxigen of the ligand VS nitrogen of the Lysine in the
> protein) using gmx distance in GROMACs (Figure 1) and VMD(figure 2)  does
> not match ?
>
>
> *Figure1.* Values obtained with gmx distance in GROMACS
>
>
>
>
> *Figure 2.* Value obtained for just one of the previous graph (green one)
> using VMD.
>
>
>
>
>
> for my believe the ligand is actually moving away (picture below).
>
>
>
>
>
> Thank you for your possible help!
>
>
>
> Best regards,
>
> Antonio
>
>
>
>
>
> p.s. to deal with PBC I first make my system “whole” , extract the first
> frame from the trajectory to use as  reference, and then use trjconv -pbc
> nojump with that first frame as reference
>
> aprun -n 1 gmx_mpi trjconv -s md_0_500.tpr -f md_0_500.xtc -o
> md_0_500_whole_dt50.xtc -pbc whole -dt 50
>
>
>
> aprun -n 1 gmx_mpi trjconv -f md_0_500_whole_dt50.xtc  -s md_0_500.tpr -b
> 0 -e 1  -o 1st_frame.gro -pbc mol –center
>
>
>
> aprun -n 1 gmx_mpi trjconv -s 1st_frame.gro -f md_0_500_whole_dt50.xtc -o
> md_0_500_whole_dt50_nojump.xtc -pbc nojump
>
>
>
>
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[gmx-users] Fwd: different vectors from gmx covar and gmx anaeig

[Qinghua Liao]

Hello,

I found out what's going on there, the first set data is the total 
vector, which I thought was


the X component.  Thanks!


All the best,

Qinghua



 Forwarded Message ---

Subject:different vectors from gmx covar and gmx anaeig
Date:   Thu, 18 Oct 2018 13:30:13 +0200
From:   Qinghua Liao 
To: gromacs.org_gmx-users@maillist.sys.kth.se



Hello,

I am doing PCA analysis to characterize the motion of a domain, I got 
the files:


average.pdb
eigenval.xvg
eigenvec.trr
covar.log

Then, with "gmx trjconv -f eigenvec.trr -s average.pdb -o eigenvec.pdb", 
I got all the vectors in the pdb file "eigenvec.pdb"


I also used "gmx anaeig -v eigenvec.trr -eig eigenval.xvg -first 1 -last 
2 -comp eigcomp.xvg " to get the first two vectors component

in "eigcomp.xvg"

I compared the vectors generated with the two commands, and I found that 
they are different.


For example, for the first vector (only the first three atoms are listed),

"eigenvec.pdb":
   x  y z
ATOM  1  N   LYS 1   0.090   0.749  -0.555  1.00 
0.00   N
ATOM  2  CA  LYS 1   0.142   0.704  -0.532  1.00 
0.00   C
ATOM  3  C   LYS 1   0.111   0.653  -0.487  1.00 
0.00   C


"eigcomp.xvg":

x
    1.    0.09367
    2.    0.08940
    3.    0.08218
y
    1.    0.00905
    2.    0.01424
    3.    0.01114
z
    1.    0.07494
    2.    0.07042
    3.    0.06526

I guess the unit is nm for both cases. Then how should I interpret this 
differences, did I do something wrong? Thanks a lot!



All the best,
Qinghua

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[gmx-users] Fwd: gmp_distance VS VMD distance analysis VS snapshot

[Antonio Carlesso]

Hi all,

I would like to take the distance over time between two pair of atoms.

I used gmx distance.

to check the value I download the snapshot every 100 ns..

When the distance is within the unit cell everything should be fine.

when the distance increase the value seems not to be correct ( comparison
between snapshot and value returned using gmx distance).

I also double check using VMD and the value seems in agreement with the
snapshot and in disagreement with gmx distance output).



Do you know how to rationalize this different distance values? and for the
same reason can I trust the interaction energy analysis that I made (ele,
vDw and sum of ele + vdW)?



I also find this thread
https://www.researchgate.net/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs
where they suggest to ask this question for clarification



Thank you for your help!
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Re: [gmx-users] Fwd: Difference between gmx spol and gmx h2order in calculationg the orientation of water around surface and solute?

[Dallas Warren]

Have you tried either?

That would be the first thing to do, try them out, see what results you
get, see if they are want you need.

On Wed, 12 Sep. 2018, 6:08 pm rose rahmani,  wrote:

> -- Forwarded message -
> From: rose rahmani 
> Date: Sun, 9 Sep 2018, 15:24
> Subject: Difference between gmx spol and gmx h2order in calculationg the
> orientation of water around surface and solute?
> To: 
>
>
> Hi,
>
> I study the properties of water molecules above surface which is in xy
> plane.
>
> I want to calculate the distribution of water polarization above surface. I
> didn't do polarizable simulation,  i just mean the orientation of dipole
> moment vector if water above surface and calculate the distributios of the
> magnitude and y-component of these vectors.
>
> I read about some gmx analyzes but i can't decide that which are really the
> best for my needs.
>
> Do you think   gmx spol  can exactly do what i want? So what could be its
> difference between gmx h2order in my case? Are they really different in my
> case? (As both of them use dipole as water representation)
>
> What about gmx sorient?
> If i have an amino acid in my system too, and i wanted to calculate the
> orientation of water dipoles around amino acid, should i use gmx spol or
> gmx sorient?
>
> I know i asked many questions in one email, but they are really really
> important and a little confusing for me. So i really would be appreciated
> if you answer  me.
>
> Best rehards
>
> Rose
> --
> 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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[gmx-users] Fwd: Gmx gangle

[rose rahmani]

-- Forwarded message -
From: rose rahmani 
Date: Sun, 9 Sep 2018, 14:45
Subject: Gmx gangle
To: 


Hi,

I want to calculate angle between water molecules and ZnS surface(slab). I
mean the angular distribution function(ADF) of ALPHA and BETA. I define to
angles; Alpha= angle between OH bond of water and  surface(plane)Beta=
angle between HOH plane and surface(plane).

I used gmax gangle for Alpha:
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
Then i selected water(SOL) group

For Beta:
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
And again i selected water group.

But results are little odd and histograms are two plot which are symmetric
plots.

I think sth is wrong. Should i make an index file for OH bond in the case
of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
calculated the angle between COM of water vector and surface not the OH
bond of water. As you know water has 2 OH bond. So... what should i do?

How about BETA? does it really calculate what i want?

Should i make an special index file?

If i want to calculate this property (ADF) in for example 1 nm from
surface, what should i do?

To be more clear, I refer you to fig.1 and fig.8
roja:
https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures

Would you please help me how can i reach these goals?

Best regards

Rose
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[gmx-users] Fwd: Difference between gmx spol and gmx h2order in calculationg the orientation of water around surface and solute?

[rose rahmani]

-- Forwarded message -
From: rose rahmani 
Date: Sun, 9 Sep 2018, 15:24
Subject: Difference between gmx spol and gmx h2order in calculationg the
orientation of water around surface and solute?
To: 


Hi,

I study the properties of water molecules above surface which is in xy
plane.

I want to calculate the distribution of water polarization above surface. I
didn't do polarizable simulation,  i just mean the orientation of dipole
moment vector if water above surface and calculate the distributios of the
magnitude and y-component of these vectors.

I read about some gmx analyzes but i can't decide that which are really the
best for my needs.

Do you think   gmx spol  can exactly do what i want? So what could be its
difference between gmx h2order in my case? Are they really different in my
case? (As both of them use dipole as water representation)

What about gmx sorient?
If i have an amino acid in my system too, and i wanted to calculate the
orientation of water dipoles around amino acid, should i use gmx spol or
gmx sorient?

I know i asked many questions in one email, but they are really really
important and a little confusing for me. So i really would be appreciated
if you answer  me.

Best rehards

Rose
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[gmx-users] Fwd: How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[rose rahmani]

-- Forwarded message -
From: rose rahmani 
Date: Mon, 10 Sep 2018, 12:58
Subject: How can i calculate the (ADF)angular distribution of the angles
between water molecule water and surface?
To: Gromacs 


Hi,
How can i calculate the angular distribution of the angles between water
molecule water and surface? surface during molecular dynamics simulation?
 is it possible by GROMACS? gmx gangle?

would you please help me?

To be clear; i refer you to these plots
https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface


Best regards

Rose
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Re: [gmx-users] Fwd: Adding new atom types

[Thomas Piggot]

I'm not sure off the top of my head. The manual says:

"Pair parameters that are not present in the [ pairtypes ] section are 
only generated when gen-pairs is set to “yes” in the [ defaults ] 
directive of forcefield.itp"


so it sounds like the parameters in the [ pairtypes ] section should be 
kept if they are there. You could check this easily yourself by running 
a simple test case through grompp and seeing what is done.


However, I should clarify/correct what I was wrote in my previous 
message as it wasn't 100 % correct (it's been a long week already!).


Rather than [ nonbonded_params ] and [ pairtypes ] sections, I was 
actually referring to the link between the values given in the [ 
atomtypes ] and [ nonbonded_params ] sections of the GROMOS 
ffnonbonded.itp files. So this is where there are up to 3 different C12 
values used to calculate the nonbonded_params for some atomtypes, as 
defined in the two tables I mentioned before in the linked paper. 
Because of the different C12 values, this is why you can't predict the [ 
nonbonded_params ] from the [ atomtypes ] using the standard combination 
rules.


For the [ pairtypes ], you also can't predict some of these from the [ 
nonbonded_params ] sections (using fudgeLJ) because some of the 
atomtypes have explicit C6/C12 values to use just for 1-4 interactions 
(as given in table 9 of the paper I linked to), while others follow the 
fudgeLJ rule (i.e. are the same as those given in the [ nonbonded_params 
] section). Because of this, you shouldn't try to generate the pairs for 
your new atomtype using gen-pairs but you should manually calculate and 
add them (as well as doing the same for the values in the [ 
nonbonded_params ] section). You should also be careful in doing these 
calculations because the C12 values given in the [ atomtypes ] section 
might not be the ones you want to use in the calculation of the 
nonbonded_params values for your new atomtype (even if your new atomtype 
only has one C12 value). That's because some of the atomtypes interact 
with themselves using the type 2 C12 values (e.g. atomtype OA), and so 
these are the values given for C12 in the [ atomtypes ] section


Hopefully that all makes sense.

Cheers

Tom

On 06/09/18 18:42, Alex wrote:

Hi Tom,
Thanks for the informative response.

For the Gromos FF the gen-pairs is "no" and then the 1-4 interactions are
taken from the parameters existed [ pairtypes ], if I change the gen-pairs
to "yes" in Gromos FF, would you please confirm me that the parameters in [
pairtypes ] is still in privilege for those interactions whose parameters
EXIST in the [ pairtypes ]? And if the parameters are not there they will
be calculated by the fudgeLJ.

Regards,
Alex

On Thu, Sep 6, 2018 at 10:58 AM Thomas Piggot  wrote:


The GROMOS force fields are somewhat different to the others in that
they provide specific 1-4 interactions by having several different C12
parameters for one atomtype (in some cases). The C12 value used depends
upon the atomtypes involved in the interactions (see tables 7 and 8 of
https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20090 for more
information for GROMOS 53A6). This means you cannot directly calculate
the pairtypes from the nonbonded_params sections of the itp as you do
not know what C12 value to use for the interaction.

This also needs to be appropriately taken into account when adding a new
atom type. You also need to explicitly add in the pairtypes, as by
having multiple potential C12 parameters means it isn't possible to
generate the pairtypes automatically.

Cheers

Tom

On 06/09/18 15:27, Alex wrote:

Dear all,

Any idea please about my both questions below?
The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the
combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule
about c12 in either sections!

Thanks.
Alex


-- Forwarded message -
From: Alex 
Date: Tue, Sep 4, 2018 at 2:43 PM
Subject: Adding new atom types
To: 


Hi all,
Two questions on which your comments would be highly appreciated;

1. What is the difference between [ nonbond_params ] and [ pairtypes ]
sections in ffnonbonded.itp file?
For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have
similar numbers for an the similar interactions when it is counted as
[ nonbond_params
] or as [ pairtypes ] because of the scale = 1, but the "OE OA"

interaction

parameters change in  [ nonbond_params ] to [ pairtypes ], similar story
for the " OA O" interaction. Which is in contrast with my
understanding of "fudgeLJ
= 1".

   [ nonbond_params ]
;   i   j   funcc6  c12

*OE  OA  1   2.261954E-031.505529E-06*
*OA  O   1   2.261954E-031.386510E-06*

[ pairtypes ]
;   i   j   funcc6  c12
*OE  OA  1   2.261954E-031.265625E-06*
*OA  O   1   2.261954E-039.687375E-07*

2. The gmx grompp gives some 

Re: [gmx-users] Fwd: Adding new atom types

[Alex]

Hi Tom,
Thanks for the informative response.

For the Gromos FF the gen-pairs is "no" and then the 1-4 interactions are
taken from the parameters existed [ pairtypes ], if I change the gen-pairs
to "yes" in Gromos FF, would you please confirm me that the parameters in [
pairtypes ] is still in privilege for those interactions whose parameters
EXIST in the [ pairtypes ]? And if the parameters are not there they will
be calculated by the fudgeLJ.

Regards,
Alex

On Thu, Sep 6, 2018 at 10:58 AM Thomas Piggot  wrote:

> The GROMOS force fields are somewhat different to the others in that
> they provide specific 1-4 interactions by having several different C12
> parameters for one atomtype (in some cases). The C12 value used depends
> upon the atomtypes involved in the interactions (see tables 7 and 8 of
> https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20090 for more
> information for GROMOS 53A6). This means you cannot directly calculate
> the pairtypes from the nonbonded_params sections of the itp as you do
> not know what C12 value to use for the interaction.
>
> This also needs to be appropriately taken into account when adding a new
> atom type. You also need to explicitly add in the pairtypes, as by
> having multiple potential C12 parameters means it isn't possible to
> generate the pairtypes automatically.
>
> Cheers
>
> Tom
>
> On 06/09/18 15:27, Alex wrote:
> > Dear all,
> >
> > Any idea please about my both questions below?
> > The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the
> > combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule
> > about c12 in either sections!
> >
> > Thanks.
> > Alex
> >
> >
> > -- Forwarded message -
> > From: Alex 
> > Date: Tue, Sep 4, 2018 at 2:43 PM
> > Subject: Adding new atom types
> > To: 
> >
> >
> > Hi all,
> > Two questions on which your comments would be highly appreciated;
> >
> > 1. What is the difference between [ nonbond_params ] and [ pairtypes ]
> > sections in ffnonbonded.itp file?
> > For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have
> > similar numbers for an the similar interactions when it is counted as
> > [ nonbond_params
> > ] or as [ pairtypes ] because of the scale = 1, but the "OE OA"
> interaction
> > parameters change in  [ nonbond_params ] to [ pairtypes ], similar story
> > for the " OA O" interaction. Which is in contrast with my
> > understanding of "fudgeLJ
> > = 1".
> >
> >   [ nonbond_params ]
> > ;   i   j   funcc6  c12
> >
> > *OE  OA  1   2.261954E-031.505529E-06*
> > *OA  O   1   2.261954E-031.386510E-06*
> >
> > [ pairtypes ]
> > ;   i   j   funcc6  c12
> > *OE  OA  1   2.261954E-031.265625E-06*
> > *OA  O   1   2.261954E-039.687375E-07*
> >
> > 2. The gmx grompp gives some errors like;
> > ERROR 1 [file topol.top, line ]
> >   No default LJ-14 types
> >
> > Which needs me to introduce new atom type ( of the problematic atoms)
> > in atomtypes.atp
> > and then in ffnonbonded.itp;
> > Would you please confirm the procedure I should take to do so;
> > First I have to add the atom type in atomtypes.atp: OC24 is an example;
> >
> > *echo "OC24 15.99940" >> atomtypes.atp*
> >
> > Then:
> > *Adding "OC248   15.999400.00A
> >0.0035644156892674973  6.222504156102231e-06" to
> > the ffnonbonded.itp/[ atomtypes ]*
> >
> > Then:
> > *Adding the ";   i   j   funcc6  c12" for the OC24
> > in ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ]*
> >
> > Do I really need to edit the ffnonbonded.itp/[ nonbond_params ] and
> > ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or
> the [
> > nonbond_params ] and [ pairtypes ] can be descided/governed by normal
> > combination rule used in the FF, so that I do not need to put them in [
> > nonbond_params ] and ffnonbonded.itp/[ pairtypes ]
> >
> > Thanks.
> > Alex
>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
> --
> 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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> 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] Fwd: Adding new atom types

[Thomas Piggot]

The GROMOS force fields are somewhat different to the others in that 
they provide specific 1-4 interactions by having several different C12 
parameters for one atomtype (in some cases). The C12 value used depends 
upon the atomtypes involved in the interactions (see tables 7 and 8 of 
https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20090 for more 
information for GROMOS 53A6). This means you cannot directly calculate 
the pairtypes from the nonbonded_params sections of the itp as you do 
not know what C12 value to use for the interaction.


This also needs to be appropriately taken into account when adding a new 
atom type. You also need to explicitly add in the pairtypes, as by 
having multiple potential C12 parameters means it isn't possible to 
generate the pairtypes automatically.


Cheers

Tom

On 06/09/18 15:27, Alex wrote:

Dear all,

Any idea please about my both questions below?
The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the
combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule
about c12 in either sections!

Thanks.
Alex


-- Forwarded message -
From: Alex 
Date: Tue, Sep 4, 2018 at 2:43 PM
Subject: Adding new atom types
To: 


Hi all,
Two questions on which your comments would be highly appreciated;

1. What is the difference between [ nonbond_params ] and [ pairtypes ]
sections in ffnonbonded.itp file?
For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have
similar numbers for an the similar interactions when it is counted as
[ nonbond_params
] or as [ pairtypes ] because of the scale = 1, but the "OE OA" interaction
parameters change in  [ nonbond_params ] to [ pairtypes ], similar story
for the " OA O" interaction. Which is in contrast with my
understanding of "fudgeLJ
= 1".

  [ nonbond_params ]
;   i   j   funcc6  c12

*OE  OA  1   2.261954E-031.505529E-06*
*OA  O   1   2.261954E-031.386510E-06*

[ pairtypes ]
;   i   j   funcc6  c12
*OE  OA  1   2.261954E-031.265625E-06*
*OA  O   1   2.261954E-039.687375E-07*

2. The gmx grompp gives some errors like;
ERROR 1 [file topol.top, line ]
  No default LJ-14 types

Which needs me to introduce new atom type ( of the problematic atoms)
in atomtypes.atp
and then in ffnonbonded.itp;
Would you please confirm the procedure I should take to do so;
First I have to add the atom type in atomtypes.atp: OC24 is an example;

*echo "OC24 15.99940" >> atomtypes.atp*

Then:
*Adding "OC248   15.999400.00A
   0.0035644156892674973  6.222504156102231e-06" to
the ffnonbonded.itp/[ atomtypes ]*

Then:
*Adding the ";   i   j   funcc6  c12" for the OC24
in ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ]*

Do I really need to edit the ffnonbonded.itp/[ nonbond_params ] and
ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or the [
nonbond_params ] and [ pairtypes ] can be descided/governed by normal
combination rule used in the FF, so that I do not need to put them in [
nonbond_params ] and ffnonbonded.itp/[ pairtypes ]

Thanks.
Alex


--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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[gmx-users] Fwd: Adding new atom types

[Alex]

Dear all,

Any idea please about my both questions below?
The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the
combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule
about c12 in either sections!

Thanks.
Alex


-- Forwarded message -
From: Alex 
Date: Tue, Sep 4, 2018 at 2:43 PM
Subject: Adding new atom types
To: 


Hi all,
Two questions on which your comments would be highly appreciated;

1. What is the difference between [ nonbond_params ] and [ pairtypes ]
sections in ffnonbonded.itp file?
For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have
similar numbers for an the similar interactions when it is counted as
[ nonbond_params
] or as [ pairtypes ] because of the scale = 1, but the "OE OA" interaction
parameters change in  [ nonbond_params ] to [ pairtypes ], similar story
for the " OA O" interaction. Which is in contrast with my
understanding of "fudgeLJ
= 1".

 [ nonbond_params ]
;   i   j   funcc6  c12

*OE  OA  1   2.261954E-031.505529E-06*
*OA  O   1   2.261954E-031.386510E-06*

[ pairtypes ]
;   i   j   funcc6  c12
*OE  OA  1   2.261954E-031.265625E-06*
*OA  O   1   2.261954E-039.687375E-07*

2. The gmx grompp gives some errors like;
ERROR 1 [file topol.top, line ]
 No default LJ-14 types

Which needs me to introduce new atom type ( of the problematic atoms)
in atomtypes.atp
and then in ffnonbonded.itp;
Would you please confirm the procedure I should take to do so;
First I have to add the atom type in atomtypes.atp: OC24 is an example;

*echo "OC24 15.99940" >> atomtypes.atp*

Then:
*Adding "OC248   15.999400.00A
  0.0035644156892674973  6.222504156102231e-06" to
the ffnonbonded.itp/[ atomtypes ]*

Then:
*Adding the ";   i   j   funcc6  c12" for the OC24
in ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ]*

Do I really need to edit the ffnonbonded.itp/[ nonbond_params ] and
ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or the [
nonbond_params ] and [ pairtypes ] can be descided/governed by normal
combination rule used in the FF, so that I do not need to put them in [
nonbond_params ] and ffnonbonded.itp/[ pairtypes ]

Thanks.
Alex
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[gmx-users] Fwd: Per species g_energy value

[Apramita Chand]

Dear All,
In my simulation system, I have one peptide with 10 cosolvent molecules and
989 water molecules. I want to have an idea of the interactions energies
between peptide-water, peptide-cosolvent etc. Using g_energy , if I obtain
a total of -687kJ interaction energy between peptide-water( coulomb+lr) ,
should I divide the value by no. of water molecules to get the value per
water molecule? Or is it a 'per peptide' value and cannot be divided by
no.of water molecules?
Please help.
Yours sincerely
Apramita Chand
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Re: [gmx-users] Fwd: free energy calculation.

[Dallas Warren]

Can't help directly, but 

Good primer for doing Gibbs energy calculations and list of references
on to read further you can find at :

http://www.alchemistry.org/wiki/Main_Page

Other place you should be looking is the literature, what have others
done and published when doing what you are doing?

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, 28 Aug 2018 at 09:38, neelam wafa  wrote:
>
> Hi everyone.
> Kindlt need your help urgently.
>
> -- Forwarded message -
> From: neelam wafa 
> Date: Mon, 27 Aug 2018, 3:41 pm
> Subject: free energy calculation.
> To: , 
>
>
> Hi!
> Dear gmx users,
> I have md simmulations of a protein with four different ligands. now I want
> to calculate the free energy of binding. which method does suit after md
> simmulation?  either g_mmpbsa or gmx BAR  method.  If I use BAR method is
> it necessary to set charges to zero as in the tutorial given at
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html.
>
> I s necessary to turn off couloumb interactions for calculating free energy
> of ligand protein complex. if i want to use coloumb interactions also then
> should i set the
>
> coul_lambdas values in the same way as vdw_lambdas.
>
> Another question is that there is another tutorial available at
> http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf
>
> In this tutorial the system has been equilliberated before generating
> the lambda states.
>
> while in the justin tutorial each lambda state is equiliberated separately.
>
> kindly tell me which one is more suitable for a protein ligand complex.
>
> looking forward for your cooperation.
>
> sorry if the questions are trivial.
>
> Regards
>
> Neelam
>
> Ph.D scholar
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[gmx-users] Fwd: free energy calculation.

[neelam wafa]

Hi everyone.
Kindlt need your help urgently.

-- Forwarded message -
From: neelam wafa 
Date: Mon, 27 Aug 2018, 3:41 pm
Subject: free energy calculation.
To: , 


Hi!
Dear gmx users,
I have md simmulations of a protein with four different ligands. now I want
to calculate the free energy of binding. which method does suit after md
simmulation?  either g_mmpbsa or gmx BAR  method.  If I use BAR method is
it necessary to set charges to zero as in the tutorial given at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html.

I s necessary to turn off couloumb interactions for calculating free energy
of ligand protein complex. if i want to use coloumb interactions also then
should i set the

coul_lambdas values in the same way as vdw_lambdas.

Another question is that there is another tutorial available at
http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf

In this tutorial the system has been equilliberated before generating
the lambda states.

while in the justin tutorial each lambda state is equiliberated separately.

kindly tell me which one is more suitable for a protein ligand complex.

looking forward for your cooperation.

sorry if the questions are trivial.

Regards

Neelam

Ph.D scholar
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[gmx-users] Fwd: "Solved the issue on annealing - so to speak "

[paul buscemi]

> 
> To work around the single point annealing I had to add three single groups.  
> Here I tried to use the first group as the ramp and the second two as constant
> 
> 
>  It turns out the number of groups the online definition gives and that mdp 
> wants  is not the number of temperature groups , but the number of molecular 
> groups.  see the grompp output below.
> 
> isolating ramps for individual molecule groups is a great advantage, but the 
> description in the mdp/options page is indeed confusing.
> 
> ==  work around with three single temperature groups ===
> 
> ; SIMULATED ANNEALING  
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing   = single single single
> 
> ; Number of time points to use for specifying annealing in each group
> annealing-npoints  = 2  2  2
> 
> ; List of times at the annealing points for each group
> annealing_time   = 0 500 0 10 0 10
> 
> ; Temp. at each annealing point, for each group.
> annealing_temp   = 100 320 320 320 320 320
> 
>   grompp  output ==
> 
> Simulated annealing for group Z8G5: Single, 2 timepoints
> Time (ps)   Temperature (K)
>   0.0  100.0
> 500.0- 320.0
> Simulated annealing for group NIGR: Single, 2 timepoints
> Time (ps)   Temperature (K)
>   0.0  320.0
>  10.0- 320.0
> Simulated annealing for group ISOP: Single, 2 timepoints
> Time (ps)   Temperature (K)
>   0.0  320.0
>  10.0- 320.0
> Number of degrees of freedom in T-Coupling group Z8G5 is 94389.77
> Number of degrees of freedom in T-Coupling group NIGR is 16199.62
> Number of degrees of freedom in T-Coupling group ISOP is 15999.62
> 
> 

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Re: [gmx-users] Fwd: problem in energy minimization

[neelam wafa]

Thanks sir Mark,

I have compared the complex before and after the minimization. there are
slight differences in the bond angles and interactions. overall posture is
not much different.
Previously I had run a simulation with same problem but the rmsd output was
stable. Are these results reliable?

Looking forward for your valuable suggestions.

Regards


On Wed, Jul 18, 2018 at 5:42 PM, neelam wafa  wrote:

> Thanks sir Mark,
>
> I have compared the complex before and after the minimization. there are
> slight differences in the bond angles and interactions. overall posture is
> not much different. I have attached  a picture of the pymol session
> comparing the two . blue one is after minimization. please have a look on
> it.
> Previously I had run a simulation with same problem but the rmsd output
> was stable.
>
> Looking forward for your valuable suggestions.
>
> Regards
>
> Neelam
>
> On Wed, Jul 18, 2018 at 9:47 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> That could be fine, as your potential energy is large and negative. We
>> can't tell from the outside. Do visualise the before and after to get some
>> clues.
>>
>> Mark
>>
>> On Tue, Jul 17, 2018, 19:11 neelam wafa  wrote:
>>
>> > -- Forwarded message --
>> > From: neelam wafa 
>> > Date: Tue, Jul 17, 2018 at 1:12 PM
>> > Subject: problem in energy minimization
>> > To: gromacs.org_gmx-users@maillist.sys.kth.se
>> >
>> >
>> > Hi,
>> >
>> > Dear gromacs users, I am running md simmulation of a protein with a
>> ligand.
>> > i have already done it with the same protein and a different ligand. Now
>> > when i run em md run i get following result.
>> >
>> > 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 150 steps,
>> > but did not reach the requested Fmax < 1000.
>> > Potential Energy  = -9.3659806e+05
>> > Maximum force =  1.0269271e+04 on atom 4399
>> > Norm of force =  9.8929054e+01
>> >
>> > NOTE: 10 % of the run time was spent in pair search,
>> >   you might want to increase nstlist (this has no effect on
>> accuracy)
>> >  please guide me is it reliable to proceede for simmulation. or there is
>> > something wrong. Is it a sign of system instability?
>> >
>> > looking forward for your cooperation.
>> >
>> > Regards
>> > --
>> > 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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>>
>
>
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Re: [gmx-users] Fwd: problem in energy minimization

[Mark Abraham]

Hi,

That could be fine, as your potential energy is large and negative. We
can't tell from the outside. Do visualise the before and after to get some
clues.

Mark

On Tue, Jul 17, 2018, 19:11 neelam wafa  wrote:

> -- Forwarded message --
> From: neelam wafa 
> Date: Tue, Jul 17, 2018 at 1:12 PM
> Subject: problem in energy minimization
> To: gromacs.org_gmx-users@maillist.sys.kth.se
>
>
> Hi,
>
> Dear gromacs users, I am running md simmulation of a protein with a ligand.
> i have already done it with the same protein and a different ligand. Now
> when i run em md run i get following result.
>
> 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 150 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -9.3659806e+05
> Maximum force =  1.0269271e+04 on atom 4399
> Norm of force =  9.8929054e+01
>
> NOTE: 10 % of the run time was spent in pair search,
>   you might want to increase nstlist (this has no effect on accuracy)
>  please guide me is it reliable to proceede for simmulation. or there is
> something wrong. Is it a sign of system instability?
>
> looking forward for your cooperation.
>
> Regards
> --
> 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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