[gmx-users] Fwd: Issue with parallel simulations in vacuum

Agusti Emperador agusti.emperador at irbbarcelona.org
Tue May 16 13:27:00 CEST 2017

Dear GROMACS experts,

I am simulating a system of two disordered proteins in vacuum. I use
gromacs 4.6.5. The serial simulation works fine, but when I run it in
parallel (2 processors) it gives seriously pathological results.

I use particle decomposition and periodic boundary conditions, because I
want to simulate a solution at a certain concentration (technically, the
simulation is in vacuum, but I have included the effects of solvation in
the nonbonded terms of the force field in my coarse-grained protein model).
Each protein has 300 particles.

I use exactly the same parameters and input files in the serial simulation
and in the parallel simulation. This is the mdp file that I use:

integrator       =  md-vv
dt               =  0.02
nsteps           =  500000000
nstxout          =  0
nstvout          =  0
nstenergy = 500000
nstlog           =  500000
nstxtcout        =  50000
nstcomm = 1
nstcalcenergy = 1
xtc-precision    =  10
rlist            =  1.4
coulombtype      =  shift
rcoulomb         =  1.2
epsilon_r        =  15
vdw-type         =  shift
rvdw-switch      =  0.9
rvdw             =  1.2
tcoupl           =  andersen
tc-grps          =  Protein
tau-t            =  .1
ref-t            =  300
Pcoupl           =  no
refcoord_scaling =  all

It works perfectly in the serial simulation, but I need to make parallel
simulations in order to simulate systems with many proteins.

How could I solve the problem?

Thank you in advance,


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