[gmx-users] atom moved too far

[Christos Deligkaris]

Justin, thank you.

I have implemented the pull code but that also exhibits the same error when
I use 12 cores (failed at about 2ns) and the simulation goes on fine when I
use 6 cores (now at about 32 ns).

I tried using the v-rescale thermostat (instead of Nose-Hoover) and
Parinello-Rahman barostat, which failed. I also tried the v-rescale
thermostat and the Berendsen barostat but that also failed. It seems to me
that this is not an equilibration issue.

So, to summarize, only if I decrease the time step to 0.001 ps or decrease
the number of cores seem to allow the calculation to proceed.

In this email list, I read that someone else was trying to use different
arguments supplied to mdrun (-nt, -ntomp etc) to solve the same problem. Is
it possible that the problem arises due to my running gmx_mpi on a single
node? This is the command I use in my submission script:

mpirun --mca btl tcp,sm,self /opt/gromacs-2018.1/bin/gmx_mpi mdrun -ntomp
\$ntomp -v -deffnm "${inputfile%.tpr}"

If you think that this is not due to a physics issue I can continue doing
calculations with 6 cores and try to install gromacs 2020 (both gmx and
gmx_mpi) to see if my problem persists there or not...


Best wishes,

Christos Deligkaris, PhD


On Thu, Jan 2, 2020 at 7:48 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/2/20 3:02 PM, Christos Deligkaris wrote:
> > thank you Justin.
> >
> > I saw on your umbrella sampling tutorial how to implement the restraints
> > using the pull code.
> >
> > The protocol I used is (if I understand correctly your question): The
> > energy minimization reached the cutoff for maximum force 1000 in 346
> steps.
> > My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 NPT
> > equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT
> > equilibration time 500ps) where I slowly decreased the position
> restraints
> > on DNA and the small molecule, as well as the harmonic restraint between
> > the two.
> > What are the best temperature coupling groups to use when we are not
> > certain whether the small molecule will spend the entire simulation
> period
> > physically bound to the macromolecule or whether it will become fully
> > solvated at some point? Is Macromolecule and Non-macromolecule the best
> > option since the small molecule will always (to a small or large extent)
> > interact with water (versus the Macromolecule_and_small_molecule and
> > everything else grouping option)?
>
> I doubt there would be a measurable or provable difference between the
> behaviors of the two setups.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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> Blacksburg, VA 24061
>
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> http://www.thelemkullab.com
>
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