Use a different box size. I replicated your problem, but your run completes
successfully with a box set up with editconf -d 1 instead of -d 3.3.
If you set nstxout = 1 during the EM process, you'll see the problematic water
molecule become unstable. It looks as if there is a small void in the solvent
(due to the way genbox tries to stack solvent configurations) and your water
molecule simply can't find a good orientation within that void.
-Justin
Ehud Schreiber wrote:
Dear GROMACS users,
When trying to simulate a pair of interacting proteins in water, I have
encountered problems that ultimately resulted in the simulation
crashing. I then tried to simplify the system as far as possible while
retaining the problem; I now believe the problem (or at least a part of
it) lies in the energy minimization step (the first molecular dynamics
one). Specifically, the forces encountered during this step are very
large, and some water molecules (which are supposed to be rigid) become
giant and misshapen.
In more details:
1) I use GROMACS version 4.0.7, single precision, on a server with two
Intel x86-64 processors and the redhat 5.4 linux OS.
2) I created a PDB file, called NaCl.pdb, with only two “atoms”,
actually Na+ and Cl- ions separated by their distance in the lattice of
salt:
HET NA A 1 1
HET CL A 1 1
HETNAM NA SODIUM ION
HETNAM CL CHLORIDE ION
FORMUL 1 NA NA 1+
FORMUL 2 CL CL 1-
HETATM 1 NA NA A 1 -1.41 0.0 0.0 1.00 0.0 NA
HETATM 2 CL CL A 1 +1.41 0.0 0.0 1.00 0.0 CL
3) I use the tip3p water model:
pdb2gmx -f NaCl.pdb -water tip3p
4) I create the box:
editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro
5) I add water using spc216, creating the saltwater.gro file (which
seems O.K. by inspection):
genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro
6) I create the energy minimization parameter file em.mdp:
------em.mdp------
integrator = steep
nsteps = 200
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
nstenergy = 10
------------------
7) I prepare the em.tpr file for the energy minimization run:
grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr
8) I run the energy minimization step:
mdrun -v -deffnm em
9) Looking at the em.log file I see that this step converged to machine
precision but did not have maximal force < 10:
…
Enabling SPC water optimization for 7561 molecules.
…
Max number of connections per atom is 2
Total number of connections is 30244
Max number of graph edges per atom is 2
Total number of graph edges is 30244
Going to use C-settle (7561 waters)
wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.075695, ra = 0.0390588
rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572
…
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
…
Steepest Descents converged to machine precision in 36 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.4678925e+05
Maximum force = 6.4623531e+05 on atom 11052
Norm of force = 5.4643726e+03
10) Looking at the em.gro file I see one monstrous water molecule (no.
3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal distance is
about 0.1 nm. Its HW2 atom (no. 11054) is close to another water
molecule (no. 5849), e.g., 0.047 nm from the latter’s HW2 atom (no. 17543):
…
3686SOL OW11052 4.348 3.778 -0.629
3686SOL HW111053 5.360 2.601 0.505
3686SOL HW211054 6.518 1.650 0.861
…
5849SOL OW17541 6.525 1.698 0.900
5849SOL HW117542 6.606 1.649 0.918
5849SOL HW217543 6.481 1.648 0.832
…
11) During the simulation, several files called stepnnl.pdb were
produced for problematic steps, where nn=11,15,19 and l=b,c. For
example, the file step19c.pdb indeed shows a problematic water molecule
no. 3686, while step19b.pdb does not. Likewise, the earlier step11c.pdb
shows a problematic water molecule no. 3266 while step11b.pdb seems
proper. The stdout/stderr of mdrun contains warnings like the following:
…
t = 0.019 ps: Water molecule starting at atom 11052 can not be settled.
Check for bad contacts and/or reduce the timestep.
…
12) Reducing the neighbor list update time, i.e., setting nstlist = 1,
does not produce any change.
13) Trying to use the conjugate gradient integrator instead of steepest
descent, i.e., setting integrator = cg, is even worse - the running crashes:
…
Step 16, Epot=-1.258771e+35, Fnorm= nan, Fmax= inf (atom 14493)
Segmentation fault
Exit 139
So, am I doing something wrong? How can I avoid these problems?
Thanks,
Ehud Schreiber.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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