[gmx-users] Help w.r.t enhancing the node performance for simulation

Dear all, Though the GROMACS was configured with MPI support during installation. installation cmake.txt I am able to use only one MPI process on the node for the simulation. This happens

Re: [gmx-users] how to restart a job in grmacs

thank you so much. On 12/27/18, sp...@iacs.res.in wrote: > - Message from SHAHEE ISLAM - >     Date: Thu, 27 Dec 2018 16:52:17 +0530 >     From: SHAHEE ISLAM > Reply-To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] how to restart a job in grmacs >       To:

Re: [gmx-users] electrostatic and LJ energy

- Message from Dr Tushar Ranjan Moharana -     Date: Thu, 27 Dec 2018 17:01:10 +0530     From: Dr Tushar Ranjan Moharana Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] electrostatic and LJ energy       To: gromacs.org_gmx-users@maillist.sys.kth.se You can use gmx energy

Re: [gmx-users] how to restart a job in grmacs

- Message from SHAHEE ISLAM -     Date: Thu, 27 Dec 2018 16:52:17 +0530     From: SHAHEE ISLAM Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] how to restart a job in grmacs       To: gmx-us...@gromacs.org thank you is the trajectory wil be from 0-15 ns or it will be

Re: [gmx-users] Question on gmx editconf, pbc and NPT (Sebastian Muraru)

I think I found a workaround my own problem: I initially placed everything in a box that includes all present molecules within its borders and solvated it. Then I redefined the box and ran an energy minimisation step. The em.gro file looks as if everything is solvated fine inside the new box

[gmx-users] electrostatic and LJ energy

You can use gmx energy (g_energy). Follow the online manual at http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-energy.html Regards -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] how to restart a job in grmacs

thank you is the trajectory wil be from 0-15 ns or it will be from 10-15 ns. On 12/27/18, sp...@iacs.res.in wrote: > - Message from SHAHEE ISLAM - >     Date: Thu, 27 Dec 2018 16:41:21 +0530 >     From: SHAHEE ISLAM > Reply-To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] how

Re: [gmx-users] how to restart a job in grmacs

- Message from SHAHEE ISLAM -     Date: Thu, 27 Dec 2018 16:41:21 +0530     From: SHAHEE ISLAM Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] how to restart a job in grmacs       To: gmx-us...@gromacs.org thank you so much for your reply. -extend 5000 what does it

[gmx-users] Question on gmx editconf, pbc and NPT

Hi there! Please help me figure something out. I have a setup made out of two molecules and I would like to investigate when happens when they meet (graphene + biomolecule). One of them is fixed by position restraints, one of them is mobile. When running a simulation under NPT conditions I

Re: [gmx-users] how to restart a job in grmacs

thank you so much for your reply. -extend 5000 what does it signify.if the time step is 2 fs then by simply multiplying these two it will give 10 ns. thanking you On 12/27/18, sp...@iacs.res.in wrote: > - Message from SHAHEE ISLAM - >     Date: Thu, 27 Dec 2018 16:16:18 +0530 >    

Re: [gmx-users] how to restart a job in grmacs

- Message from SHAHEE ISLAM -     Date: Thu, 27 Dec 2018 16:16:18 +0530     From: SHAHEE ISLAM Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] how to restart a job in grmacs       To: gmx-us...@gromacs.org hi, i have run a simulation for 10 ns but after 4 ns due to power off

[gmx-users] how to restart a job in grmacs

hi, i have run a simulation for 10 ns but after 4 ns due to power off the job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi md_0_10ns.cpt,continue the left simulation.Now after normal termination of 10 ns how i wll do the next 5 ns simulation after this 10 ns. thanking you shahee --