Thanks for replying so fast. Sent using Boxer
On Feb 11, 2016 2:05 PM, Mark Abraham <[email protected]> wrote: Hi, That's up to the author of the tutorial. Smaller list sizes are faster to run, and if the purpose of the EM is to ensure that equilibration succeeds, then anything that works, works. Mark On Thu, Feb 11, 2016 at 11:28 AM M S <[email protected]> wrote: > I thought the tutorial set the em parameters lower than nvt parameters > based on a specific reason. So there is no specific reason in tutorial? > > Best regards > > Sent using Boxer > > On Feb 11, 2016 12:22 PM, Mark Abraham <[email protected]> wrote: > > Hi, > > On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr <[email protected] > > > wrote: > > > Dear all users, > > > > In mdp files in ligand tutorial, rvdw,rlist.are equal to 1 in em step,. > > And are equal to 1.4 in nvt,npt and production md > > > > When we can set different interaction parameters for different step? > > > > You should choose such parameters based on those used for the > parametrization of the force field, and/or subsequent reports of successful > applications of them, particularly by the original authors. > > As you no doubt learned from the tutorial, EM is commonly used for relaxing > inconsistencies in the starting geometry so that equilibration can proceed > stably. Experience shows that short-range settings that are ultra faithful > to the force field do not materially improve the success of equilibration - > anything normally does the job fine. > > Mark > > Best regards > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
