Thanks Justin for the information. By the way, Could you please give me a hint on the release of new GPU-version (4.6)?
On Thu, Oct 11, 2012 at 4:20 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/10/12 11:53 PM, Venkat Reddy wrote: > >> Dear all, >> I am doing a protein-ligand simulation and following Justin's tutorials. I >> have confusion in passing check point file to the next step in position >> restrain simulation (during NPT). I am slowly releasing the restraints >> during NPT simulation, *viz., 1000....100.....10....1....**noPR*. So, >> during >> >> NPT-PR, is it required to pass the check-point file generated in the >> previous step to the next step (1000....100....10...1....**noPR)? or is >> it >> fine if I use directly the check point file generated during NPT-no PR >> step >> to final MD step? >> >> > You seem to be asking two questions, so it's not really a matter of "or." > One should always pass the final checkpoint of the previous stage of > simulation to the current stage. So during your reduction of restraints, > you should pass the checkpoint from the previous restraint strength. At > the outset of MD, you should pass the checkpoint from whatever the step > immediately prior to it was, which, from the description, is NPT in the > absence of restraints. > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing list gmx-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 www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
