[gmx-users] Re: A bug for MPI of GROMACS?
Mark.Abraham at anu.edu.au
Wed Aug 12 05:38:27 CEST 2009
> Dear Mark and Vitaly,
> In order to get help, here I describe the more detailed procedure.
> I successfully generated the gro and top files using pdb2gmx.
> pdb2gmx -f -o -p -ter
> And also the grompp finished successfully.
> grompp -f -c -p -o
> Then I ran the mdrun in parallel way, only to find that the polymer became many pieces.
I doubt that it did. The representation of it that you were viewing may
have made what was one topology look like many pieces.
> mpirun -np 4 mpimdrun -s -o -c -e -g -v
> Obviously, it cannot form any bonds between those pieces due to the long distances.
> With the same tpr file,I ran the mdrun in non-parallel-way, however, the polymer seems to behave properly.
> mdrun -s -o -c -e -g -v
> The partial files (gro, top, and mdp) are given as follows:
> gro file:
> Great Red Owns Many ACres of Sand
> 1DIA N1 1 -0.199 0.069 0.078
> 125AMI H42 1382 -0.073 -0.681 -1.613
> 3.61500 4.27230 2.77190
Since you are doing simulating a periodic system, are these box
> top file:
> [ molecules ]
> ; Compounds #moles
> Protein_D 1
> mdp file:
> define = -DFLEXIBLE
> constraint = none
> integrator = steep
> nsteps = 10000
> ns_type = grid
> nstcgsteep = 100
> nslist = 10
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.0
> DispCorr = EnerPres
> fourierspacing = 0.36
> pme_order = 4
> ewald_rtol = 1e-5
> emtol = 10
> emstep = 0.01
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