[gmx-users] Problem with running crystal simulation

Elton Carvalho eltonfc at gmail.com
Mon Nov 23 21:24:29 CET 2015

Hello, Ben.

Looks like your box blew up [
http://www.gromacs.org/Documentation/Terminology/Blowing_Up ].

It would be useful to know the initial box size and how well the
minimization converged (were the forces low enough? How was the box
pressure?). Are you sure the box size is adequate for your cristal? Is it
adequate for your cutoffs (the shortest box vector should be ~2 times the
cutoff AFAIK)?

If you are trying to run an NPT simulation right after the EM, I'd advise
for an NVT thermalization first, so you can equilibrate the temperature and
forces before messing up with box dimensions and pressures. If your system
blows up in NVT, that's a symptom of bad topology. If it doesn't blow up in
NVT and does in NPT, check your pressure options in the MDP: "pcoupl",
"pcoupltype", "tau_p", "ref_p" and "compressibility".

Is your topology correctly connecting the atoms through the box wall so you
have a periodic molecule? Have you set "periodic_molecules = yes" in your
MDP files?

Elton Carvalho

On Mon, Nov 23, 2015 at 3:58 PM, Ben Tam <btam125 at hotmail.co.uk> wrote:

> Dear GROMACS user,
> I have a problem here when I am trying to run a crystal simulation, this
> is the warning I am getting from the error file:
> Warning: Only triclinic boxes with the first vector parallel to the x-axis
> and the second vector in the xy-plane are supported.         Box (3x3):
>         Box[    0]={         inf,         -nan,         -nan}
> Box[    1]={        -inf,          inf,         -nan}            Box[
> 2]={        -nan,         -nan,          inf}         Can not fix pbc.
> And it terminate the run as segmentation fault.
> I was able to gmx grompp it without any error, also I was able to run
> minimisation but not md. Therefore can anyone tell me what's wrong with my
> simulation? I have no idea which file to attach so apologise for that.
> Best regards,
> Ben
> --
> 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.

More information about the gromacs.org_gmx-users mailing list