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

[Mark Abraham]

wuxiao wrote:
> 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
>  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

Since you are doing simulating a periodic system, are these box
dimensions reasonable?

Mark

>   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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