Thank you very much for your help. Olga
בתאריך יום א׳, 20 בינו׳ 2019 ב-22:35 מאת Mark Abraham < mark.j.abra...@gmail.com>: > Hi, > > They're inactive so whether they have any value or are present does not > matter. > > Mark > > On Sun., 20 Jan. 2019, 10:34 Olga Press, <pres...@post.bgu.ac.il> wrote: > > > Dr. Mark Abraham, thank you so much for your help. > > That meaning that in the NPT equilibration without position restrains > > the refcoord_scaling should not be present at all in the mdp file*?* > > > > Thank you in advance. > > Olga > > > > בתאריך יום א׳, 20 בינו׳ 2019 ב-11:06 מאת Mark Abraham < > > mark.j.abra...@gmail.com>: > > > > > Hi, > > > > > > If you're not using position restraints then options that affect how > they > > > work are inactive. > > > > > > Mark > > > > > > On Sun., 20 Jan. 2019, 09:46 Olga Press, <pres...@post.bgu.ac.il> > wrote: > > > > > > > Dear gromacs users, > > > > > > > > I perform membrane-protein simulation and used the same mdp files as > > > > suggested by the tutorial of Dr. Justin Lemkul with one exception of > > > > changing the correct parameters for charmm36ff as suggested > > > > by gromacs manual. > > > > > > > > I performed 10ns of *NVT equilibration with position restrained* on > the > > > > protein and found a convergence of the temperature to the desired > > > > temperature. Followed by 50ns of *NPT equilibration with position > > > > restrained *on the protein, and after that, I performed 100ns of > *NPT > > > > equilibration without position restraint*. > > > > My question is, in the *NPT equilibration without the position > > restrain,* > > > > what should I put in the category of *refcoord_scaling? com? *or > > > should I > > > > delete it as I found in the MD.mdp file in the tutorial? > > > > > > > > Thanks in advance, > > > > Olga > > > > -- > > > > 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 gmx-users-requ...@gromacs.org. > > > > > > > -- > > > 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 gmx-users-requ...@gromacs.org. > > > > > -- > > 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 gmx-users-requ...@gromacs.org. > -- > 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.