Hi, Check your box size,I had a same problem. I used a larger box then the problem solved.
Best Ali On Mon, Oct 30, 2017 at 6:29 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > How big is the system before and after? Gro format used fixed columns, so > can sometimes struggle with large systems. Try using .g96 as the output > file extension > > Mark > > On Mon, 30 Oct 2017 17:29 <smritiaishwary...@gmail.com> wrote: > > > Checked the file again. It is the one that gets generated after the > > solvation command is run. > > > > Sent from my iPhone > > > > > On 30-Oct-2017, at 9:39 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > > Hi, > > > > > > The most likely scenario is that you are looking at a gro file that is > > not > > > the one that was written by the solvation tool. > > > > > > Mark > > > > > > On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti < > > > smritiaishwary...@gmail.com> wrote: > > > > > >> Hi! > > >> > > >> I'm trying to solvate a system of a CNT and a protein molecule. My > > updated > > >> topology file shows 106275 new solvent molecules added but the .gro > file > > >> has only coordinates for 6197 new molecules. I'm using SPC model for > > >> solvating, Please help. > > >> > > >> Regards, > > >> Aishwarya Smriti > > >> Senior Undergraduate > > >> Chemical Engineering > > >> Indian Institute of Technology, Delhi > > >> -- > > >> 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.