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

[Mark Abraham]

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
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