[gmx-users] domain decomposition

Dear all, I am simulating a system consisting urea molecules. After successfully generating tpr file while I am trying to run mdrun, the following error is appearing. Fatal error: There is no domain decomposition for 72 ranks that is compatible with the given box and a minimum cell size of

Re: [gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?

This is an issue with CGenFF, nothing to do with GROMACS. So you need to ask this question through the CGenFF help channel(s), wherever that may be. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal

[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?

Hi All, I have created a crystal structure of 2 polymer chains (PEG) and I need to calculate the cohesive energy for my system using CHARMM36 FF. In this case my fix_mol2 file includes 2 ligands, to convert to str file I get the following error: readmol2 warning: non-unique atoms were

[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?

Hi All, I have created a crystal structure of 2 polymer chains (PEG) and I need to calculate the cohesive energy for my system using CHARMM36 FF. In this case my fix_mol2 file includes 2 ligands, to convert to str file I get the following error: readmol2 warning: non-unique atoms were

Re: [gmx-users] Error when running pbs files using GROMACS on hpc cluster

On 8/20/19 5:56 PM, Anh Vo wrote: Hi everyone, I have submitted pbs files to run GROMACS on a high performance computing cluster, but I received error files showing these messages: "... librdmacm: Warning: couldn\'t read ABI version. librdmacm: Warning: assuming: 4 librdmacm:

Re: [gmx-users] Gromacs FEP tutorial

On 8/20/19 1:36 PM, Alex Mathew wrote: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html The protocol in the tutorial is simply the elimination of LJ parameters to compute the vdW contribution to free energy of solvation. It is not (by

[gmx-users] Error when running pbs files using GROMACS on hpc cluster

Hi everyone, I have submitted pbs files to run GROMACS on a high performance computing cluster, but I received error files showing these messages: "... librdmacm: Warning: couldn\'t read ABI version. librdmacm: Warning: assuming: 4 librdmacm: Fatal: unable to open /dev/infiniband/rdma_cm

Re: [gmx-users] Gromacs FEP tutorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html > -- 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] Charmm36M neutral C-terminal Proline

On Tue, Aug 20, 2019 at 9:44 AM Akshay wrote: > Hello All, > > I seem to be having a very particular issue with the Charmm36M force-field > available at http://mackerell.umaryland.edu/charmm_ff.shtml. The issue > occurs when using pdb2gmx's -ter flag and selecting a neutral COOH terminal > when

[gmx-users] gpu usage

Dear Users, I am getting reasonable performance from two rtx -2080ti's - AMD 32 core and on another node two gtx-1080 ti's -AMD 16 core i.e 20-30 ns/day with 30 atoms. But in all my runs the % usage of the gpu's is typcially 40% to 60 % . Given that it is specialized software, I notice

Re: [gmx-users] WARNING

If your trajectory has position information, then yes, it can be used to compute potential energies. > Thank you for your reply sir. In this case can I use .The file to compute > potential energies. > > On Tue 20 Aug, 2019, 4:40 PM Mark Abraham, > wrote: > >> Hi, >> >> You're doing a rerun from

Re: [gmx-users] typedefs.h in gromacs installation

Hi, You can use only GROMACS versions that gromos++ supports. Hopefully they've documented which ones those are :-) Mark On Tue, 20 Aug 2019 at 15:47, Johannes Hermann wrote: > Hi Justin, > > Thanks! So this is a gromos++ problem? The gromos++ developers should > update the linking during

Re: [gmx-users] typedefs.h in gromacs installation

Hi Justin, Thanks! So this is a gromos++ problem? The gromos++ developers should update the linking during installation, right? All the best Johannes On 20.08.19 15:11, Justin Lemkul wrote: On 8/20/19 8:56 AM, Johannes Hermann wrote: Dear all, I am currently installing gromos++

[gmx-users] Charmm36M neutral C-terminal Proline

Hello All, I seem to be having a very particular issue with the Charmm36M force-field available at http://mackerell.umaryland.edu/charmm_ff.shtml. The issue occurs when using pdb2gmx's -ter flag and selecting a neutral COOH terminal when the C-terminal residue is a Proline. Then, when subsequent

Re: [gmx-users] WARNING

Thank you for your reply sir. In this case can I use .The file to compute potential energies. On Tue 20 Aug, 2019, 4:40 PM Mark Abraham, wrote: > Hi, > > You're doing a rerun from a trajectory file that probably doesn't have > velocities in it. mdrun can compute potential energies from the

Re: [gmx-users] simulation on 2 gpus

Dear Szilard, thanks for the very clear answer. Following your suggestion I tried to run without DD; for the same system I run two simulations on two gpus: gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 -gputasks 00 -pin on -pinoffset 0 -pinstride 1 gmx mdrun -deffnm run2 -nb

Re: [gmx-users] AVX_512 and GROMACS

On Mon, Aug 19, 2019 at 12:00 PM tarzan p wrote: > > Hi all.I have a dual socket Xeon GOLD 6148 which has the capabilities for > > Instruction Set Extensions Intel® SSE4.2, Intel® AVX, Intel® AVX2, Intel® > AVX-512 > but hen why si gromacs giving the error for AVX_512 but takes AVX2_256??? >

Re: [gmx-users] typedefs.h in gromacs installation

On 8/20/19 8:56 AM, Johannes Hermann wrote: Dear all, I am currently installing gromos++ analysis software. When I link my Gromacs 2018.6 or 2016.6 installation, I get the error: ../../contrib/gromacs2gromos.cc:101:30: fatal error: gromacs/typedefs.h: No such file or directory However,

Re: [gmx-users] Error Report

Thank you very much sir. I will check On 8/18/19, Justin Lemkul wrote: > > > On 8/18/19 2:06 PM, Dr Adekunle Rowaiye wrote: >> Hello all, >> I need help. I got this while doing simulation. What do I do? >> >> File input/output error: >> protein_pr.gro > This means that either (1) if this is an

[gmx-users] typedefs.h in gromacs installation

Dear all, I am currently installing gromos++ analysis software. When I link my Gromacs 2018.6 or 2016.6 installation, I get the error: ../../contrib/gromacs2gromos.cc:101:30: fatal error: gromacs/typedefs.h: No such file or directory However, if I link my gromacs 5.1.4 installation

Re: [gmx-users] Tetrahedral order parameter

On 8/20/19 7:51 AM, Omkar Singh wrote: Hello gromacs users, I am working on protein-water system. I am trying to calculate top(tetrahedral order parameter) by "gmx hydorder" command. After finding xpm how to proceed for xvg format. gmx hydorder does not produce such output. You may want to

Re: [gmx-users] "comm-mode = Angular" gives error

On 8/20/19 5:21 AM, Jorden Cabal wrote: Hi Justin, Thank you for your response. In my case the cost of increasing simulation box is very large. I have already tried it by keeping distance between the periodic images of the macromolecule up to 50 Angstrom. Could you suggest me any other option

Re: [gmx-users] question on ffG43a1p force field

On 8/20/19 2:11 AM, Lei Qian wrote: Thank you Dr. Lemkul, Could I ask one more question? Thank you! When I did the step for adding ions and minimization and equilibration steps, one warning always showed up. So I had to add -maxwarn 2 after the command gmx grompp. This warning is as follows:

Re: [gmx-users] Analysing multiple cavities in ion Channel through CompEl simulations

Hi Carlos, > Am 20.08.2019 um 13:12 schrieb Carlos Navarro : > > Dear gmx-users, > I'm currently investigating ion permeability in a channel that displays > multiple cavities through ComEl simulations. Unfortunately one can just > define a single cylinder per membrane. Yes, this counting of ion

[gmx-users] Tetrahedral order parameter

Hello gromacs users, I am working on protein-water system. I am trying to calculate top(tetrahedral order parameter) by "gmx hydorder" command. After finding xpm how to proceed for xvg format. Thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Mailing list for Postdoctoral opportunities in Simulations

you can go to ccl.net I am also looking for the postdoctoral position in biological molecule simulations Warm Regards Akhil Kumar Research Associate IISc Bangalore INDIA. #09839263326 On Tue, Aug 20, 2019 at 11:55 AM Peter Mawanga < peter.mawanga.la...@gmail.com> wrote: > Hello everyone > >

[gmx-users] Analysing multiple cavities in ion Channel through CompEl simulations

Dear gmx-users, I'm currently investigating ion permeability in a channel that displays multiple cavities through ComEl simulations. Unfortunately one can just define a single cylinder per membrane. Considering the size of my system (>440k atoms) I don't think is a viable idea to run n independent

Re: [gmx-users] WARNING

Hi, You're doing a rerun from a trajectory file that probably doesn't have velocities in it. mdrun can compute potential energies from the position coordinates, but these other quantities can't be computed from just the position coordinates. mdrun can't know what you're expecting to be correct,

[gmx-users] WARNING

Dear all, During the calculation of interaction energy i found one warning WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present.But in the quilibration step the temp

Re: [gmx-users] "comm-mode = Angular" gives error

Hi Justin, Thank you for your response. In my case the cost of increasing simulation box is very large. I have already tried it by keeping distance between the periodic images of the macromolecule up to 50 Angstrom. Could you suggest me any other option to do this. In Gromacs, rotation around

[gmx-users] Mailing list for Postdoctoral opportunities in Simulations

Hello everyone Can someone please send me mailing list addresses where I could get updates on Postdoctoral positions available in the field of simulations. -- Cheers Peter -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] question on ffG43a1p force field

Thank you Dr. Lemkul, Could I ask one more question? Thank you! When I did the step for adding ions and minimization and equilibration steps, one warning always showed up. So I had to add -maxwarn 2 after the command gmx grompp. This warning is as follows: WARNING 1 [file topol.top, line 48]: