Thank you Justin
On Wed, Jun 27, 2012 at 9:36 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 6/27/12 4:30 PM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I am wondering whether would you advise to run NVT, NPT (position >> restrained) and before the pulling simulation e.g of the ligand from >> protein-ligand complex? As I saw in Justin tutorial he equilibrate the >> system with only NPT ensemble before pulling. Is that really sufficent >> e.g. for 200 ps? >> > > There is no catch-all equilibration scheme that works universally. NVT and > NPT are commonly run in sequence. My systems in the tutorial are quite > robust and a single NPT phase is sufficient. Please do not assume that this > is universally true. Your protocol should be based on how stable your > systems are and how well your desired observables converge, but that much is > true of every simulation. > > -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