[gmx-users] Problem with running crystal simulation

[Ben Tam]

Hi Elton,
Thank you for your reply. I have increase my box size to 10 10 10. However it is still blowing up. Yes I am trying to run NPT simulation, will freezing the crystal framework will cause the box to blow up? Because I am doing an adsorption simulation hence I need the crystal stay in certain place. 

Best regards,
Ben

> From: eltonfc at gmail.com
> Date: Mon, 23 Nov 2015 17:23:58 -0300
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem with running crystal simulation
> 
> 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?
> 
> Cheers,
> -- 
> 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
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