[gmx-users] REMD system blowing up

Hi all, I would like to know if there is a way to figure out which of the replica is exploding during REMD simulation? I am running REMD for 54 replicas and the system is exploding with just one step14495b.pdb and step14495c.pdb files. Does this mean there is just one replica that is exploding?

[gmx-users] Fw: question about kalp15 in dppc justin tutorial

- Forwarded Message - From: ‪neda razavi‬ ‪ To: "" Sent: Monday, 28 September 2015, 22:50:04 Subject: question about kalp15 in dppc justin tutorial when we run grompp command one of the outputs is mdout.mdp. can we use these

[gmx-users] Fw: problem with kalp in dppc simulation justin tutorial

- Forwarded Message - From: ‪neda razavi‬ ‪ To: "gmx-us...@gromacs.org" Sent: Monday, 28 September 2015, 22:54:24 Subject: problem with kalp in dppc simulation justin tutorial     In the simulation of KALP15 in DPPC , why the

[gmx-users] Excessive memory usage of mdrun

Good morning, I'm trying to simulate a protein system on an HPC cluster called Orchestra, that use gromacs 5.0.4. The system size is 39126 atoms and is made by the protein, 12160 water molecules, one Na+ and one Cl-. Of this system I've already made a run of 50 ns on my workstation without

Re: [gmx-users] Fw: question about kalp15 simulation in dppc

On 9/28/15 4:12 PM, ‪neda razavi‬ ‪ wrote: - Forwarded Message - From: ‪neda razavi‬ ‪ To: "gmx-us...@gromacs.org" Sent: Monday, 28 September 2015, 22:47:10 Subject: question about kalp15 simulation in dppc in simulation

Re: [gmx-users] CNT in water

On 9/27/15 5:18 PM, maryam haji wrote: Dear Users, I want to simulate CNT in water solvent with CHARMM27 force field. The used parameters for simulation of CNT follows: The .n2t file is: CCA0.0012.011 3C 0.141 C 0.141 C 0.141 CCA0.0012.011 2C 0.141

[gmx-users] File input/output error

Dear Gromacs-users, I am trying to run simulation of a protein on our CRAY XC40 supercomputer and while running simulation (using mdrun) for nvt npt simulations, and production runs, I am getting the following error: File input/output error: Cannot rename checkpoint file; maybe you are out of

[gmx-users] question

Dear gromacs users I am doing md simulation of rna-ligand system using gromacs 5.0.5. In equilibration phase (NVT), I encountered with following error? GROMACS: gmx mdrun, VERSION 5.0.5 Executable: /share/apps/gromacs/bin/gmx Library dir: /share/apps/gromacs/share/gromacs/top Command

[gmx-users] question

I obtained my lig.gro using editconf and lig.itp using antechamber. I added lig.gro to conf.gro (for RNA). I included lig.itp to topolo.top file. Double sids (704, 705) for atom 2525 Double sids (704, 705) for atom 2526 Double sids (704, 705) for atom 2527 Double sids (704, 705) for atom 2528

[gmx-users] Gromacs GPU got hang

Hi All, I am new in using Gromacs. I have a small HPC cluster and one of the nodes has a Tesla K40 GPU. Now I have problem when trying to run a Gromacs GPU job in that GPU node. It seems my job got hang after several hours running, the gromacs log was stopped being updated and through nvidia-smi

Re: [gmx-users] maestro cms file to gromacs

A quick and dirty way to do it is to load the cms file into vmd (or other reader) and save a copy as pdb, then use pdb2gmx. This may give you trouble, in which case you will need to hand write a topology file and then use one of the other tools on the pdb verison of your system to make a .gro

Re: [gmx-users] No domain decomposition

Hi Chandan, I tried it once using -nt option but it failed . I kept it 8 although I dont know how to change the number of nodes for mdrun correctly. How do I know the value of x if I want to run say mdun -deffnm mdfinal -nt x. It is worth mentioning here that for my NPT and NVT

Re: [gmx-users] adding walls? to EDL simulation?

hello users, here is another and better phrasing of my problem. if i have a 3D pbc I create some sort of "dipol plate". And using only pbc=xy I can not use Ewald methods (PME) or pressure coupling (manual) without using two walls. I don't understand the wall-atomtype variable? And how to use

[gmx-users] question

Dear Justin, Thanks for your quick answer. I want to know about 704, 705 in following line: Double sids (704, 705) for atom 2525 Double sids (704, 705) for atom 2526 Double sids (704, 705) for atom 2527 Double sids (704, 705) for atom 2528 Double sids (704, 705) for atom 2529 Double sids (704,

Re: [gmx-users] No domain decomposition

g_tune_pme would give some useful information. On Mon, Sep 28, 2015 at 6:05 PM, soumadwip ghosh wrote: > Hi Chandan, > I tried it once using -nt option but it failed . I > kept it 8 although I dont know how to change the number of nodes for > mdrun

Re: [gmx-users] No domain decomposition

On 9/28/15 8:49 AM, Chandan Choudhury wrote: g_tune_pme would give some useful information. On Mon, Sep 28, 2015 at 6:05 PM, soumadwip ghosh wrote: Hi Chandan, I tried it once using -nt option but it failed . I kept it 8 although I dont know

[gmx-users] (no subject)

In simulation of kalp15 in Dppc why should we remove the initial periodicity of kalp15 before packing the lipids around the protein? -- 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] Fw: question about kalp15 in dppc justin tutorial

On 9/28/15 4:13 PM, ‪neda razavi‬ ‪ wrote: - Forwarded Message - From: ‪neda razavi‬ ‪ To: "" Sent: Monday, 28 September 2015, 22:50:04 Subject: question about kalp15 in dppc justin tutorial when we run grompp command one

[gmx-users] (no subject)

 In simulation of KALP15 in DPPC, when we run grompp command one of the outputs is mdout.mdp. can we use these files for our energy minimization step, after making necessary changes? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Error on doing a restart

Im trying to do a restart in a MD on gromacs 5 and geting this error, "error while loading shared libraries : libgmxpreprocess". Someone know what is happening? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before