[gmx-users] Box size error during attempted NPT equilibration

Andrew DeYoung adeyoung at andrew.cmu.edu
Mon May 30 18:02:07 CEST 2011


I have tried to run a simulation of 1000 SPC/E water molecules.  I have a
PDB file containing a 10 by 10 by 10 regular array (cube) of water
molecules, each separated by approximately 6 Angstroms.  I used pdb2gmx to
convert the PDB file to GRO and topology, selecting the OPLS-AA force field
and the SPC/E water model.  I then used editconf to adjust the box size to a
cube of edge length 60 Angstroms (using the option -box 6.0 6.0 6.0 in
editconf, because the -box option takes arguments of units in nm, I think).
I chose an edge length of 60 Angstroms because by looking at the GRO file,
it seems that the largest position coordinate is ~54 Angstroms, so a box
with edge length 60 Angstroms should, I think, contain all of the 1000 water

I then ran energy minimization (steep integrator, emtol = 1000.0 kJ/mol/nm,
emstep = 0.01 nm, nsteps = 50000), and steepest descents converged to Fmax <
1000 in one single step.  The final potential energy was -3333 kJ/mol, the
final maximum force was 11 kJ/mol/nm, and the final norm of force was 8
kJ/mol.  It seems a little strange to me that this minimization converged in
only one step, but I guess that this means that the water molecules were
placed far enough away from each other to begin with. 

Then I ran an NPT equilibration, and after about 1.5*10^6 steps, the
simulation crashed and I got the following error message:

Program mdrun, VERSION 4.5.4
Source code file: domdec.c, line: 2861

Fatal error:
The X-size of the box (4.000392) times the triclinic skew factor (1.000000)
is smaller than the number of DD cells (8) times the smallest allowed cell
size (0.500000)

If you have time, do you have any idea about what was the cause of this

If I understand correctly, the error message seems to be telling me that
(4.000392*1) < (8*0.5).  Could it be that my box size is fluctuating too
much during this attempted NPT equilibration, leading to the crash?  Or
perhaps my value of tau_p (tau_p = 2.0 ps) is too large?

To summarize, I am trying to do a 5 ns NPT equilibration (5*10^6 steps of
0.001 ps each) with the md integrator, Nose-Hoover temperature coupling, and
Berendsen pressure coupling.  Should I next try V-rescale temperature
coupling instead of Nose-Hoover, since Florian Dommert pointed out to me the
other day that
V-rescale tends to be more stable?

The complete input file that I used for equilibration is as follows:
; npt-eq.mdp
; NPT Equilibration (5 ns)
title = OPLS Water NPT equilibration

integrator = md
nsteps = 5000000
dt = 0.001

nstxout = 250
nstvout = 250
nstenergy = 250
nstlog = 250

ns_type = grid
nstlist = 1
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0

coulombtype = PME
pme_order = 4
fourierspacing = 0.12

tcoupl = nose-hoover
tc-grps = system
tau_t = 0.1
ref_t = 298

pcoupl = berendsen
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5

pbc = xyz

DispCorr = no

gen_vel = yes
gen_temp = 298
gen_seed = 173529

Also, the commands I used for equilibration are:

grompp -f npt-eq.mdp -c em.gro -p water.top -o npt-eq.tpr -po npt-eqout.mdp
mdrun -v -deffnm npt-eq -cpo npt-eq.cpt

Thank you very much for your time!  I really appreciate it.

Andrew DeYoung
Carnegie Mellon University

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