Re: [gmx-users] Average exchange probability when extending REMD
Hi, Yes, if you need that, this is the thing to do. The only place mdrun records any of that is the .log file, and of course that is not re-read in the next stage.You also want to avoid/manage mdrun's appending feature, because IIRC that throws away all that end-of-log-file output when the next run starts. Mark On Wed, Jun 15, 2016 at 3:47 PM OuyangYanhua <15901283...@163.com> wrote: > Sorry, I am a little confused, what you mean is that the gromacs cannot > automatically combine the data of the both in the replica exchange > statistics section. Maybe myself need write some program to combine the > first part data and the extended data to get the average probability of > whole REMD? > > 在 2016年6月15日,下午9:34,Mark Abraham 写道: > > > > Hi, > > > > That's never been implemented, unfortunately. > > > > Mark > > > > On Wed, Jun 15, 2016 at 3:25 PM OuyangYanhua <15901283...@163.com> > wrote: > > > >> Hi, > >> I extended the REMD of a protein in a explicit water and append the data > >> to the old ones and it appended. However, at the end of the .log files, > the > >> replica exchange statistics section only contains the data of extended > >> time, it did not combine the former statistics and the extended > >> statistics. why? and how to combine the both statistics. > >> > >> Best regards, > >> Ouyang > >> -- > >> 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.
Re: [gmx-users] Average exchange probability when extending REMD
Sorry, I am a little confused, what you mean is that the gromacs cannot automatically combine the data of the both in the replica exchange statistics section. Maybe myself need write some program to combine the first part data and the extended data to get the average probability of whole REMD? > 在 2016年6月15日,下午9:34,Mark Abraham 写道: > > Hi, > > That's never been implemented, unfortunately. > > Mark > > On Wed, Jun 15, 2016 at 3:25 PM OuyangYanhua <15901283...@163.com> wrote: > >> Hi, >> I extended the REMD of a protein in a explicit water and append the data >> to the old ones and it appended. However, at the end of the .log files, the >> replica exchange statistics section only contains the data of extended >> time, it did not combine the former statistics and the extended >> statistics. why? and how to combine the both statistics. >> >> Best regards, >> Ouyang >> -- >> 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.
Re: [gmx-users] Average exchange probability when extending REMD
Hi, That's never been implemented, unfortunately. Mark On Wed, Jun 15, 2016 at 3:25 PM OuyangYanhua <15901283...@163.com> wrote: > Hi, > I extended the REMD of a protein in a explicit water and append the data > to the old ones and it appended. However, at the end of the .log files, the > replica exchange statistics section only contains the data of extended > time, it did not combine the former statistics and the extended > statistics. why? and how to combine the both statistics. > > Best regards, > Ouyang > -- > 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.