[gmx-users] gmx rdf not reading gmx checked trr file.

[Jones de Andrade]

Hi all.

I'm having a problem with gmx rdf in some trajectories of mine.

I'm dealing with several mixtures of two solvents in different concentrations. 
While I was dealing with the "non-infine dilutions", or when I had several 
molecules of each, gmx rdf calculated the rdfs with no error.

Now, I'm having the following error, only in trajectories where I have one 
molecule of one solvent and 999 of the other. I also would like to point out 
that I tested gmx check on the trajectories in question, with absolutely no 
failure identified in the trr files.

##

---
Program: gmx rdf, version 2018
Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 228)
Function:void gmx::TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()

System I/O error:
Could not read coordinates from trajectory

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

##

Does anybody have an idea on what is going wrong?

Thanks a lot in advance.
-- 
Jones de Andrade
(jdandr...@iq.ufrgs.br)
DFQ/IQ/UFRGS
Lattes: http://lattes.cnpq.br/6675936210583999
Orcid: https://orcid.org/-0003-3429-8119

Enviado pelo K-9 mail
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Re: [gmx-users] Fatal Error when launching gromacs 2019.2 on GPU.

[Szilárd Páll]

Hi,

This is an issue in one of pre-detection checks that trips due to
encountering exclusive / prohibited mode devices.

You can work around this by entirely disabling the detection using the
GMX_DISABLE_GPU_DETECTION environment variable.

Cheers,
--
Szilárd


On Thu, Oct 17, 2019 at 5:01 PM Artem Shekhovtsov 
wrote:

> Hello!
> Problem: The launch of mdrun that does not require video cards exit with
> fatal error if at least one video card is busy on the host at that time.
> gmx mdrun -deffnm test -ntmpi 1 -ntomp 1 -nb cpu -bonded cpu
> ---
> Program: gmx mdrun, version 2019.2
> Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100)
>
> Fatal error:
> cudaFuncGetAttributes failed: all CUDA-capable devices are busy or
> unavailable
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> I have this error in gromacs version 2019.2, 2019.3, 2020.beta.
> Version - 2018.6 is not affected.
> All version builds with the same flags.
>
> Archive with log files and gromacs build files
>
> https://drive.google.com/file/d/1ahn7S69CU5yvAPlLWHryXmMzcGfdWVxP/view?usp=sharing
>
>
> I would appreciate any help.
>
> Thanks,
> Artem Shekhovtsov.
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Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Justin Lemkul]

On 10/25/19 7:43 AM, Amit Jaiswal wrote:

Dear Jorden,

I tried the simulation by changing the residue number in .itp file but 
it still goes out of the box during NVT. As Justin mentioned that the 
naming of the residue is irrelevant, so I guess either I am doing some 
minor mistake in


I had no issue with the name of the residue, I was pointing out that 
there is only one valid atom *number* that can be in posre_zn.itp. It's 
quite straightforward to apply the restraint (and fairly obvious when 
it's wrong because grompp will throw a fatal error).


Are you sure that this "movement" of the ion is not simply a PBC effect? 
Depending on your box shape, you may have to re-image very carefully.


-Justin

topology naming. So, I have included the order of topology file below. 
Please Have a look and let me know if there is something wrong. I have 
no idea why Zn ion is so hard to restrain. Thanks for your time.

*; Include Position restraint file*
*#ifdef POSRES*
*#include "posre.itp"*
*#endif*
*; Include ZN position restraints*
*#ifdef POSRES_ZN*
*#include "posre_zn.itp"*
*#endif*
*; Include ligand topology*
*#include "nad.itp"*
*; Ligand position restraints*
*#ifdef POSRES_LIG*
*#include "posre_nad.itp"*
*#endif*
*; Include water topology*
*#include "./charmm36-mar2019.ff/tip3p.itp"*
*#ifdef POSRES_WATER*
*; Position restraint for each water oxygen*
*[ position_restraints ]*
*; i funct fcx fcy fcz*
*1 1 1000 1000 1000*
*#endif*
*; Include topology for ions*
*#include "./charmm36-mar2019.ff/ions.itp"*
*[ system ]*
*; Name*
*Protein in water*
*[ molecules ]*
*; Compound #mols*
*Protein_chain_A 1*
*ZN 1*
*NAD 1*
*SOL 12908*
*NA 4*
Regards,
Amit
23.10.2019, 20:41, "Justin Lemkul" :



On 10/22/19 12:04 AM, Amit Jaiswal wrote:

 Dear Jorden,
 Thanks for your reply. As you have suggested, i found there is a
 mismatch of the atom number in the zn.itp file and the .gro
file. I
 have included few residues of .gro file for your convenience.
 What i understand is that I have to rename the zn.itp file with
 residue no. 4265 and not 2220. Please correct me if I am wrong.


The global atom number is irrelevant in defining position restraints
(and will actually trigger a warning in your case). If Zn is
defined as
a separate [moleculetype] in its own .itp file, the only valid atom
number for position restraints is 1. See

http://manual.gromacs.org/current/user-guide/run-time-errors.html#atom-index-n-in-position-restraints-out-of-bounds

-Justin

 And also you suggested me to "minimize the system very
carefully".
 What do you mean by this? Should i use lesser minimisation
steps ?
 Thanks for your time and efforts.
 With kind regards,
 Amit
 391THR HG22 4260 4.897 5.356 3.136
 391THR HG23 4261 4.889 5.247 2.993
 391THR C 4262 4.600 5.071 3.244
 391THR OT1 4263 4.599 5.012 3.355
 391THR OT2 4264 4.496 5.082 3.173
 392ZN ZN 4265 7.278 6.612 5.838
 393NAD PA 4266 6.217 7.359 2.802
 393NAD O1A 4267 6.090 7.410 2.863
 393NAD O2A 4268 6.337 7.451 2.808
 393NAD O5B 4269 6.185 7.331 2.647
 393NAD C5B 4270 6.082 7.233 2.620
 19.10.2019, 21:53, "Jorden Cabal" mailto:jordenca...@gmail.com>>:

 Dear Amit,
 Your files look correct to me. If "2220" atom in your
coordinate
 file is
 the "Zn" atom, it should not be displaced because, from
your mdp
 file and
 topology setting you have restrained all the heavy atoms of
 Protein, Nad
 and Zn. I don't understand why it is happening. Even the
 restraining force
 you are taking is good enough.
 I suggest you to check if the atom number 2220 in the
co-ordinate file
 (.gro file) is Zn atom or not? If it is not then you have
wrongly
 selected
 atom number for restraining. Also, if you are following
the standard
 tutorial for energy minimization which do not restrain
any atom, I
 suggest
 you to check the position of Zn atom in structure you get
after energy
 minimization. If the location of Zn ion is changed during
the EM,
 then you
 will need to minimize the system very carefully.
 Hope this will fix your issue.
 Thank you

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Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Amit Jaiswal]

Dear Jorden,I tried the simulation by changing the residue number in .itp file but it still goes out of the box during NVT. As Justin mentioned that the naming of the residue is irrelevant, so I guess either I am doing some minor mistake in topology naming. So, I have included the order of topology file below. Please Have a look and let me know if there is something wrong. I have no idea why Zn ion is so hard to restrain. Thanks for your time. ; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif ; Include ZN position restraints#ifdef POSRES_ZN#include "posre_zn.itp"#endif ; Include ligand topology#include "nad.itp" ; Ligand position restraints#ifdef POSRES_LIG#include "posre_nad.itp"#endif ; Include water topology#include "./charmm36-mar2019.ff/tip3p.itp" #ifdef POSRES_WATER; Position restraint for each water oxygen[ position_restraints ]; i funct fcx fcy fcz1 1 1000 1000 1000#endif ; Include topology for ions#include "./charmm36-mar2019.ff/ions.itp"  [ system ]; NameProtein in water [ molecules ]; Compound #molsProtein_chain_A 1ZN 1NAD 1SOL 12908NA 4 Regards,Amit  23.10.2019, 20:41, "Justin Lemkul" :On 10/22/19 12:04 AM, Amit Jaiswal wrote: Dear Jorden, Thanks for your reply. As you have suggested, i found there is a mismatch of the atom number in the zn.itp file and the .gro file. I have included few residues of .gro file for your convenience. What i understand is that I have to rename the zn.itp file with residue no. 4265 and not 2220. Please correct me if I am wrong.The global atom number is irrelevant in defining position restraints(and will actually trigger a warning in your case). If Zn is defined asa separate [moleculetype] in its own .itp file, the only valid atomnumber for position restraints is 1. Seehttp://manual.gromacs.org/current/user-guide/run-time-errors.html#atom-index-n-in-position-restraints-out-of-bounds-Justin  And also you suggested me to "minimize the system very carefully". What do you mean by this? Should i use lesser minimisation steps ? Thanks for your time and efforts. With kind regards, Amit 391THR HG22 4260 4.897 5.356 3.136 391THR HG23 4261 4.889 5.247 2.993 391THR C 4262 4.600 5.071 3.244 391THR OT1 4263 4.599 5.012 3.355 391THR OT2 4264 4.496 5.082 3.173 392ZN ZN 4265 7.278 6.612 5.838 393NAD PA 4266 6.217 7.359 2.802 393NAD O1A 4267 6.090 7.410 2.863 393NAD O2A 4268 6.337 7.451 2.808 393NAD O5B 4269 6.185 7.331 2.647 393NAD C5B 4270 6.082 7.233 2.620 19.10.2019, 21:53, "Jorden Cabal" : Dear Amit, Your files look correct to me. If "2220" atom in your coordinate file is the "Zn" atom, it should not be displaced because, from your mdp file and topology setting you have restrained all the heavy atoms of Protein, Nad and Zn. I don't understand why it is happening. Even the restraining force you are taking is good enough. I suggest you to check if the atom number 2220 in the co-ordinate file (.gro file) is Zn atom or not? If it is not then you have wrongly selected atom number for restraining. Also, if you are following the standard tutorial for energy minimization which do not restrain any atom, I suggest you to check the position of Zn atom in structure you get after energy minimization. If the location of Zn ion is changed during the EM, then you will need to minimize the system very carefully. Hope this will fix your issue. Thank you -- 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 gmx-users-requ...@gromacs.org>.  --==Justin A. Lemkul, Ph.D.Assistant ProfessorOffice: 301 Fralin HallLab: 303 Engel HallVirginia Tech Department of Biochemistry340 West Campus Dr.Blacksburg, VA 24061jalem...@vt.edu | (540) 231-3129http://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 visithttps://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] how to select head groups of lipid within 10 angstrom of protein

[Justin Lemkul]

On 10/25/19 5:38 AM, Peter Stern wrote:

You are probably causing your command to run in the background with “&”.  Try 
using “and” instead.


In addition to this, the selection string needs to be enclosed by single 
quotes.


-Justin


Peter

Sent from my iPhone


On Oct 25, 2019, at 11:45 AM, SHAHEE ISLAM  wrote:

Hi,
I am trying to calculate the angle between P and N vector of my lipid
(popc+popg) with regards to the z axis to see how the protein is affecting
the membrane. I am using this command, but it does not working
gmx select -f *.xtc -s *.tpr -select POPG & name P* N* within 1.0 of
Protein -oi number.dat
but the problem is, when the command is running only
  gmx select -f *.xtc -s *.tpr -select POPG
this command.
Can anyone please guide me what i am doing wrong.
Thanking you
Shahee
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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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Re: [gmx-users] how to select head groups of lipid within 10 angstrom of protein

[Peter Stern]

You are probably causing your command to run in the background with “&”.  Try 
using “and” instead.  

Peter

Sent from my iPhone

> On Oct 25, 2019, at 11:45 AM, SHAHEE ISLAM  wrote:
> 
> Hi,
> I am trying to calculate the angle between P and N vector of my lipid
> (popc+popg) with regards to the z axis to see how the protein is affecting
> the membrane. I am using this command, but it does not working
> gmx select -f *.xtc -s *.tpr -select POPG & name P* N* within 1.0 of
> Protein -oi number.dat
> but the problem is, when the command is running only
>  gmx select -f *.xtc -s *.tpr -select POPG
> this command.
> Can anyone please guide me what i am doing wrong.
> Thanking you
> Shahee
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[gmx-users] Obtaining stress-strain curves: Parrinello-Rahman, anisotropic and deform

[Nigel Hew]

Hi all, I’m pretty new to Gromacs and would like to obtain the stress-strain 
curves for a CH4/CO2 hydrate system where I apply the strain in one direction 
and obtain the corresponding stresses. Would someone be able to explain the use 
of the deform option and the corresponding pressure and compressibility values 
to be used with this option? I have been going through the manual and have 
tried looking for examples online but have failed to find any useful examples. 
Any help with this and useful references is much appreciated. 

Thanks,
Nigel 

Sent from Mail for Windows 10

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[gmx-users] how to select head groups of lipid within 10 angstrom of protein

[SHAHEE ISLAM]

Hi,
I am trying to calculate the angle between P and N vector of my lipid
(popc+popg) with regards to the z axis to see how the protein is affecting
the membrane. I am using this command, but it does not working
gmx select -f *.xtc -s *.tpr -select POPG & name P* N* within 1.0 of
Protein -oi number.dat
but the problem is, when the command is running only
  gmx select -f *.xtc -s *.tpr -select POPG
this command.
Can anyone please guide me what i am doing wrong.
Thanking you
Shahee
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Re: [gmx-users] QM/MM run tips or tutorials (Bogdanov, Vladimir)

[Groenhof, Gerrit]

Dear Vlad,

Tutorials can be found at http://wwwuser.gwdg.de/~ggroenh/software.html

Although the tutorials are outdated and were designed for much older version of 
GROMACS, most steps can still be run. Besides, the tutorials should help 
getting familiar with the QM/MM input.

A newer tutorial, but unfortunately designed for the upcoming QM/MM interface 
between GROMACS and CP2K and thus made for CP2K is found 
here:https://github.com/vavmodi/Summer_School-2019

I hope these materials help,

Gerrit


> 
> Hi all,
> 
> I would like to try Gromacs 2018 with QM. I am good enough with running MD on 
> Gromacs, but have never used QM. Any tips how to get started or any links to 
> tutorials will be very helpful.
> 
> Best regards,
> Vlad
> 
> 

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