[gmx-users] Molecule specific explosion

[Mark Abraham]

Hi,

What happens when you use this topology on a single molecule? Other
standard techniques for diagnosing at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Mark

On Tue, Apr 28, 2015 at 8:09 AM, Eric Smoll <ericsmoll at gmail.com> wrote:

> Hi Mark,
>
> Thanks for the reply. In my previous message, one molecular component of my
> liquid solution greatly-deforms ("explodes") on  energy minimization. I
> have examined the topology and everything seems in order. No warnings were
> generated by grompp or mdrun. Here are my minimization settings:
>
> constraints=h-bonds
> integrator=steep
> emtol=1000.0
> emstep=0.01
> nsteps=10000
> nstlist=10
> nstxout=1
> ns_type=grid
> rlist=1.5
> coulombtype=PME
> rvdw=1.5
> rcoulomb=1.5
> pbc=xyz
> cutoff-scheme=verlet
> nstcalclr=1
>
> The liquid topology file is generated by pdb2gmx using aminoacids and I
> detect no errors.
>
> Best,
> Eric
>
> On Sun, Apr 26, 2015 at 2:08 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Look at the whole molecule topology. Don't ignore any warnings.
> >
> > Mark
> > On 26/04/2015 9:38 am, "Eric Smoll" <ericsmoll at gmail.com> wrote:
> >
> > > Hello Gromacs Users,
> > >
> > > I have constructed a multi-component solution and, during energy
> > > minimization, one molecule type is radically deforming under ~ 0.2 ps.
> > All
> > > molecules of this type "explode" simultaneously. Looking over the
> > topology,
> > > all the atoms in this molecules appear to have correct forcefield
> > > assignments. I am writing to ask if anyone might have a suggestion on
> > how I
> > > can identify the origin of this problem.
> > >
> > > Best,
> > > Eric
> > > --
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