[gmx-users] Box size error during attempted NPT equilibration
Andrew DeYoung
adeyoung at andrew.cmu.edu
Mon May 30 18:02:07 CEST 2011
Hi,
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
molecules.
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
crash?
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
(http://lists.gromacs.org/pipermail/gmx-users/2011-May/061716.html)
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)
; NO POSITION RESTRAINT
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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