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

[Justin Lemkul]

On 5/16/17 7:26 AM, Agusti Emperador wrote:
> 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?
>

What is the problem?  What do you define as "seriously pathological results" in 
this case?  Also note that 4.6.5 is practically prehistoric and you may wish to 
consider a newer, faster, less-buggy version of the code.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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