[gmx-users] atom moved too far

[Christos Deligkaris]

dear all,

While running my production run of a small molecule noncovalently bound to
DNA in water, I got the error:

Step 8921600:

Atom 20338 moved more than the distance allowed by the domain decomposition
(0.457738) in direction X

distance out of cell 0.495788

New coordinates:    3.304    4.938    2.969

Old cell boundaries in direction X:    0.000    0.715

New cell boundaries in direction X:    0.000    0.709


-------------------------------------------------------

Program:     gmx mdrun, version 2018.1

Source file: src/gromacs/domdec/domdec.cpp (line 4076)

MPI rank:    0 (out of 12)


Fatal error:

An atom moved too far between two domain decomposition steps

This usually means that your system is not well equilibrated

The error occured at about time=18 ns. I erased the output files,
resubmitted the calculation again from the beginning time=0 and in that
attempt the error appeared at about 16 ns. In both cases it was an atom of
a water molecule that moved too far.

I read the "gromacs blow up" webpage and thought maybe the harmonic
intermolecular constraints I have on the cap base pairs are too strong for
the time step of 0.002 so I decreased the time step to 0.001ps and that
calculation is now at about 60 ns (still running). I also tried using only
6 cores with a step of 0.002 (I used 12 cores in the two failed
calculations) and that calculation is now at time=50ns (still running).

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.

I implemented the harmonic restraint between the small molecule-DNA and the
cap base pairs using the following in the topology (just showing one
example)

[ intermolecular_interactions ]

[ bonds ]

455     483      6       0.18564  200

For the production run, I use

comm-mode = Linear

nstcomm = 100

comm-grps = System


cutoff-scheme = Verlet

nstlist = 10

coulombtype = PME

rcoulomb = 1.2

vdwtype = Cut-off

vdw-modifier = Potential-shift

rvdw = 1.2

rvdw-switch = 0

DispCorr = no

tcoupl = nose-hoover

nh-chain-length = 1

nsttcouple = -1

tc-grps = DNA_NNK Water_and_ions

tau-t = 0.4 0.4

ref-t = 300 300

pcoupl = Parrinello-Rahman

pcoupltype = isotropic

tau-p = 1.0

ref-p = 1.0

refcoord-scaling = com

constraints = h-bonds

constraint-algorithm = lincs

I believe SETTLES is included in the TIP3P topology by default so I am
using that also.

I have run three 50 ns production runs of the small molecule in water
without any problems (NPT equilibration was done in 1 calculation for these
three).

I was surprised that the two failed calculations did not fail at exactly
the same time step (start with same positions, velocities and solve
determinist equations of motion).

The error message suggests that the system was not well equilibrated.
Should I try doing my NPT equilibrations over 1 ns instead of 500ps?

Is it possible that using as a temperature coupling group the
macromolecule-small molecule results in the blow up if the small molecule
ends up leaving the macromolecule? (I did see the small molecule becoming
fully solvated at some point in the trajectory of the failed calculations)

Using a force constant of 200 kJ/mol/nm is perhaps too large for a time
step of 0.002 ps? (I think I tried removing the harmonic restraints between
the two bases on the cap base pairs and that calculation also failed). And
I have seen in the literature a time step of 0.002 ps is reasonable for DNA
and DNA-ligand calculations.

It is not clear to me why using less cores allows the calculation to
proceed (unless it got to 50ns by chance and it will blow up eventually).

Best wishes,

Christos Deligkaris, PhD
Assistant Professor of Physics, University of Southern Indiana
SC2220, 8600 University Blvd, Evansville IN, 47712
Office Phone: (812) 228-5056
www.deligkaris.org @DeligkarisGroup