[gmx-users] Encountered with error after executing the command "gmx solvate"

[Mark Abraham]

Hi,

Please see the reference manual for discussion of the minimum image
convention.

Otherwise, your report sounds like a bug in gmx solvate. Please open an
issue at redmine.gromacs.org and attach a tarball of files that reproduce
the issue.

Mark

On Wed, 13 Jan 2016 13:15 Seera Suryanarayana <palusoori at gmail.com> wrote:

> Dear gromacs users,
>
> I have been trying to simulate the xtal structure which is homo tetramer
> and each chain has more than 400 amino acids. after editconf where I have
> used the cubic box with -c -d 1.0. After this command I have executed the
> following command..
>
> gmx solvate -cp 4pv1.gro -cs spc216.gro -o 4cp1_solv.gro -p topal.top
>
> and I got the error as ..
>
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or
> box_yy-|box_zy| or box_zz has become smaller than the cut-off.
>
> When I checked the gromacs archive somewhere mentioned that violating
> minimum image convention. I don't understand what does it mean. Kindly tell
> me why this error is encountered and how do I resolve it?
>
> Thanks in advance
> Surya
> Graduate student
> 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-request at gromacs.org.
>