Re: [gmx-users] Need protein-ligand free energy calculation tutorial

2013-09-19 Thread Sergey Filkin
. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sergey Filkin, Researcher -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re: [gmx-users] Re: general question about molecule.rtp and pdb2gmx

2013-08-27 Thread Sergey
Yes, can remove. However, ability to remove don't depend on our desire, but depend on Force field set of rules. If molecule was parametrized with 1-4 LJ, it is not desirable to remove it. If it is in-house force field which ignore 1-4 LJ, then one can safely remove it. Sergey 27.08.201

Re: [gmx-users] shell MD

2013-07-05 Thread Sergey
your problem correlate with that discussion, perhaps? > > Dr. Vitaly V. Chaban > > On Fri, Jul 5, 2013 at 1:58 PM, Sergey wrote: > >>  In case of MD run. Minimization procedure was successful. >> >>  05.07.2013, 14:48, "Dr. Vitaly Chaban" : >>>

Re: [gmx-users] shell MD

2013-07-05 Thread Sergey
In case of MD run. Minimization procedure was successful. 05.07.2013, 14:48, "Dr. Vitaly Chaban" : > In which case can the determinant not be computed? > > Dr. Vitaly V. Chaban > > On Thu, Jul 4, 2013 at 10:53 AM, Sergey wrote: > >>  Dear users, >> >

Re: [gmx-users] shell MD

2013-07-04 Thread Sergey
; Checkpointing helps you continue after crashes ;nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 emtol= 0.8 04.07.2013, 12:53, "Sergey" : > Dear users, > > I

[gmx-users] shell MD

2013-07-04 Thread Sergey
including .mdp file ? Sergey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the ww