Re: [gmx-users] energy minization mdp

Dear Sir Thank you very much. It is working now. On Fri, Jul 28, 2017 at 4:16 PM, Justin Lemkul wrote: > > > On 7/28/17 2:54 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear User >> >> I have protein-ligand system. I have basic idea for energy >> minimization.mdp >>

[gmx-users] gmx bar

Hi gromacs users, I'm using gmx bar to plot my free energy calculation results with the command: gmx bar *xvg -o -oh -oi I obtain the graphic bar.xvg where DG are reported on Y axis and the number of lambda steps (0,1,2,3...) on the X. I'd like to get a graphic where the values of my lambdas

Re: [gmx-users] problem on Gromacs 4.5.7 installation

Hi, Please don't do new work with buggy software that was de-supported over four years ago. I have a hard time imagining some science done with 4.5.7 that is worth extending now, and needs that version to do so. Regardless, in order to help, we need more detail than "it doesn't work." Mark On

Re: [gmx-users] How to increase the volatile gpu-util

Hi, Yes. The simulation quality is not determined by nstlist, but rather by the buffering implemented by the list. You've chosen a (default) tolerance to set the quality you require, and if you also choose nstlist then mdrun will choose the buffer size necessary to honour that tolerance. See

[gmx-users] problem on Gromacs 4.5.7 installation

Hi, I'am a phd student, i need to work with gromacs version 4.57 but i have an installation problem, i apply all the instructions of installation but i have always the 'make install' problem. I really need to work with gromacs (4.5.7) for my work Best regards -- *Rahma Dahmani Doctorante

Re: [gmx-users] How to increase the volatile gpu-util

Hi, There is not much to be done with an RF simulation. The GPU is idle when doing search, update and constraints. You could try a higher nstlist, as the message reports, eg gmx mdrun -nstlist 25 but you'll only get a small improvement. The way to get better utilisation, if your science needs