[gmx-users] Number of coordinates in .gro file does not match topology

[Ali Ahmed]

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.abraham at 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 <smritiaishwarya85 at 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.abraham at 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 <
> > > smritiaishwarya85 at 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-request at 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-request at 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-request at 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-request at gromacs.org.
>