[gmx-users] Molecule specific explosion

[Eric Smoll]

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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