[gmx-users] OpenMM

PACIELLO GIULIA giulia.paciello at polito.it
Tue Apr 13 16:23:23 CEST 2010

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,

More information about the gromacs.org_gmx-users mailing list