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.
