[gmx-users] Re: A bug for MPI of GROMACS?

[wuxiao]

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.
  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
 1382
    1DIA  N1  1  -0.199  0.069  0.078
    ......
    125AMI H42  1382 -0.073  -0.681  -1.613
     3.61500  4.27230  2.77190

  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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