Hi all,
I'm using the Application Programming Interface openMM for
executing molecular dynamics simulations with Gromacs on
an NVIDIA GTX 295 GPU (here is installed CUDA SDK for
issuing and managing computations on GPU).
Even if I have followed all the instructions reported for
the correct installation of GPU, CUDA, OpenMM and even if
my .mdp file for the simulation is written following the
features supported in the release Gromacs-OpenMM, the
output of the serial code running on CPU is quite
different from that of the parallel code running on GPU
(.gro files).
Looking at the .log file I have also noticed that the
energy terms 'Angle', 'Proper
Dih.''Ryckaert-Bell.','LJ-14'Coulomb-14', 'LJ (SR)',
'Coulomb (SR), 'RF excl', are null for the simulation
performed with the parallel code.
I obtained these results during different simulations on
several .pdb files. I used, for example, '1AKI.pdb' file,
downloaded from the Protein Data Bank. I decided to choose
ffamber94 force-field (even if this is more suitable for
nucleic acids) and I treated the structure with an energy
minimization of 1 ps and a position restraint of 5 ps.
After these, I executed the md simulation using the
following .mdp file as input for the mdrun-openmm program:
cpp = /lib/cpp
include = -I../top
integrator = md
dt = 0.002
nsteps = 10000
nstlist = 5
ns_type = grid
rlist = 1.2
pbc = xyz
coulombtype = Reaction-Field
rcoulomb = 1.2
vdwtype = switch
rvdw_switch = 1.0
rvdw = 1.1
tcoupl = no
Pcoupl = no
gen_vel = no
constraints = all-bonds
I have performed a lot of simulations using even different
options for the .mdp file (coulombtype, pbc...), but I
have never obtained the expected results.
Someone can help me?
Thanks a lot,
Giulia
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