[gmx-users] Molecule specific explosion

[Eric Smoll]

Hi Mark,

Good question. I have rerun the simulation using a single molecule in a box
without periodic boundary conditions and I see an identical distortion
during energy minimization. Most of the suggestions present in
http://www.gromacs.org/Documentation/Terminology/Blowing_Up describe
instability during MD. I am seeing this extreme geometry distortion much
earlier during equilibriation.

Best,
Eric

On Tue, Apr 28, 2015 at 3:38 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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