OK, I got it. But how can I get a .xtc output of NPT or NVT equilibration? The output of mdrun -deffnm npt doesn't have any .xtc files to visualize by VMD. I have seen that I get .xtc file just after the final mdrun -deffnm md (as you said).
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Thursday, August 9, 2012 10:52 PM Subject: Re: [gmx-users] Visualizing a process On 8/9/12 2:21 PM, Shima Arasteh wrote: > > > You mean I can not see the NPT equilibration process! > I mean exactly what I said. You can load the .xtc file as data for a coordinate file in, e.g. VMD, and watch the movie of the simulation after it is complete. -Justin > > Sincerely, > Shima > > > ----- Original Message ----- > From: Justin Lemkul <jalem...@vt.edu> > To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS > users <gmx-users@gromacs.org> > Cc: > Sent: Thursday, August 9, 2012 10:45 PM > Subject: Re: [gmx-users] Visualizing a process > > > > On 8/9/12 2:12 PM, Shima Arasteh wrote: >> Hi, >> >> Is it possible to view the process of a NPT or NVT equilibration? Which >> command in gromacs can generate a .xtc output? >> > > Only mdrun writes .xtc files of simulations. As far as I know, one cannot > watch the simulation in real time but .xtc files can be visualized in a > variety of viewing programs after the simulation is complete. > > -Justin > > -- ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
