Each time I try to run mdrun with double precision and more than one node, I
always receive some atom with infinite Fmax, no matter what I do, Always on
Step=0. The strangest thing is that it still attempts the minimization but
the values never change except for Dmax in a steepest descent. If I change
the coordinates of the atom that has the inf value another one has infinite
value and so on. I use lam/mpi, with the command 'mpirun -np 5 mdrun_d -v
-deffnm potd'. My double precision was configured with both --enable-mpi and
--enable-double. Here is a copy of the mdp file I use:
title = potd
cpp = /usr/bin/cpp
constraints = none
integrator = steep
nsteps = 0
ns_type = grid
nstcomm = 1
nstlist = 10
rlist = 1.4
coulombtype = Shift
vdw_type = Shift
rcoulomb = 1.2
rvdw = 1.2
rcoulomb_switch = 1.0
rvdw_switch = 1.0
epsilon_r = 6.0
optimize_fft = yes
emtol = 1000
emstep = 0.01
nstcgsteep = 100
It doesn't matter if it is in vaccum or water. I have minimized to an emtol
of 10 and mdrun_d still does not work. I am using gromacs 3.3.1. I have
tried changing or removing almost every value in the mdp file. I have tried
different pdb files. Tried using grompp and grompp_d. Tried with -sort
-shuffle and without. Is this another one of those compiler issues like
genion? Any help would be great.
Thanks,
Josiah Zayner
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