Hi, Take a configuration of interest, strip the solvent, put it in a box you think is good, and re-equilibrate just like you did before you started.
Mark On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > > Yes, I did when I started the simulation. The box size I used to start the > simulation was very big(I was dealing with an unknown sample). After > successfully generating the configurations I realized that further work > could move faster if I could trim the box size little bit now. > So is there any way now to reduce the box size and proceed with relevant > configurations towards PMF generation ? > Please suggest me a way here. > > Thank you. > > On Apr 24, 2017 12:22 AM, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: > > > Hi, > > > > You get to choose the box size eg with editconf when you set up your > > simulation. It's not pre-defined ;-) > > > > Mark > > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal <abhisek.m...@gmail.com> wrote: > > > > > Hello, > > > > > > Another thing I wanted to ask. > > > After generating configurations I found out that the predefined box > size > > > (used to reach so far) is excessively high. > > > Is it possible to trim the box size to perform further mdrun during > > > umbrella sampling? > > > > > > Please suggest me a way, it is taking very long time with current box > > size. > > > > > > Thank you. > > > > > > > > > > > > On Apr 23, 2017 10:02 PM, "Mark Abraham" <mark.j.abra...@gmail.com> > > wrote: > > > > > > > Hi, > > > > > > > > You can only load a trajectory with fewer frames. Either don't write > so > > > > many, or filter it with trjconv first. > > > > > > > > Mark > > > > > > > > On Sun, 23 Apr 2017 17:20 abhisek Mondal <abhisek.m...@gmail.com> > > wrote: > > > > > > > > > Hi, > > > > > I'm having a problem loading trajectory file after umbrella > sampling. > > > The > > > > > file is so huge in size that the VMD finally runs out of memory. > I'm > > > > > operating with 125gb of physical memory here though. > > > > > > > > > > Is there any way out of it ? > > > > > > > > > > > > > > > Thank you > > > > > -- > > > > > Abhisek Mondal > > > > > > > > > > *Senior Research Fellow* > > > > > > > > > > *Structural Biology and Bioinformatics Division* > > > > > *CSIR-Indian Institute of Chemical Biology* > > > > > > > > > > *Kolkata 700032* > > > > > > > > > > *INDIA* > > > > > -- > > > > > 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. > -- 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.