Re: [gmx-users] NVT, NPT and then pulling?
Thank you Justin On Wed, Jun 27, 2012 at 9:36 PM, Justin A. Lemkul 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 listgmx-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
Re: [gmx-users] NVT, NPT and then pulling?
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 listgmx-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] NVT, NPT and then pulling?
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? Thanks, Steven -- gmx-users mailing listgmx-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
