Hi All,
I am thinking of running an implicit solvent simulation using Gromacs
(.mdp file pasted at the end of the email). However, I am a bit
concerned about its accuracy as I get different results for the
Polarisation term. More specifically, the first step of an energy
minimisation gives different values for this energy term depending on
the number of threads/processes that I use (while the rest of the E.
terms are exactly the same). I tried the Intel compilers + MKL, and the
GNU compilers + ACML, as well as GMX versions 5.0.4 and 5.1-beta1. I
could even get a segfault with the GNU compilers and ACML when using 2
"processes" (gmx mdrun -nt 2).
The question is simple. Am I doing anything wrong? Is there any
precaution that I should take?
Cheers,
Albert
-----------------------------------------------
; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps
to perform
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor
list and long range forces
cutoff-scheme = Group
ns_type = grid ; Method to determine neighbor list
(simple, grid)
coulombtype = Cut-Off ; Treatment of long range
electrostatic interactions
rcoulomb = 999.0 ; Calculate all long range interactions
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = no ; Periodic Boundary Conditions (yes/no)
; Implicit solvent parameters:
implicit-solvent = GBSA ; use implicit solvent
gb-algorithm = OBC ; use the OBC approach for the GB
radius
gb-obc-alpha = 1 ; parameters correspond to OBC-II
gb-obc-beta = 0.8 ;
gb-obc-gamma = 4.85 ;
gb-epsilon-solvent = 78.5 ; as seen in the original paper.
sa-algorithm = Ace-approximation ; include surface area
contribution for non-polar atoms
sa-surface-tension = 0.0054 ; default value.
--
---------------------------------
Dr Albert Solernou
EPSRC Research Fellow,
Department of Physics and Astronomy,
University of Leeds
Tel: +44 (0)1133 431451
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