[gmx-users] MD simulation on 1 and 4 nodes

[Alexander Zuev]

Dear all,

the results of my run with 10 ps MD simulation on 1 and 4 nodes are
differed from each other:
1) from gro-file after mdrun with np=1:
    2GLU      N   16   1.171   0.770   0.983  0.1916 -0.1159 -0.3137
    2GLU      H   17   1.143   0.813   0.897 -1.2392 -0.6945 -0.1708
    2GLU     CA   18   1.226   0.869   1.077 -0.0526 -0.1020 -0.1841
    2GLU     CB   19   1.234   1.005   1.007  0.3661 -0.2199 -0.3691
    2GLU     CG   20   1.102   1.058   0.951  0.5377  0.3099 -0.2806
    2GLU     CD   21   1.089   1.009   0.807  0.7168 -0.5444 -0.0134
    2GLU    OE1   22   1.016   0.917   0.765 -0.4520  0.5124 -0.3375
    2GLU    OE2   23   1.158   1.069   0.721  0.1797 -0.1854 -0.1970
    2GLU      C   24   1.151   0.875   1.210  0.1965 -0.0042 -0.0464
    2GLU      O   25   1.029   0.880   1.225  0.2254  0.3574  0.0764

2) from gro-file after mdrun with np=4:
    2GLU      N   16   1.141   0.738   0.989  0.1650 -0.2755 -0.3296
    2GLU      H   17   1.096   0.790   0.917  0.0641  0.4210  0.2319
    2GLU     CA   18   1.219   0.822   1.081 -0.3070 -0.2080  0.0118
    2GLU     CB   19   1.273   0.934   0.991 -0.0205  0.1246  0.5967
    2GLU     CG   20   1.177   1.045   0.949  0.0338 -0.1540 -0.2860
    2GLU     CD   21   1.068   0.995   0.855 -0.2075  0.6878 -0.4600
    2GLU    OE1   22   1.106   0.961   0.741  0.0894  0.5117 -0.3091
    2GLU    OE2   23   0.950   1.003   0.895 -0.0805 -0.3430  0.1321
    2GLU      C   24   1.150   0.869   1.209 -0.3185 -0.1466 -0.0169
    2GLU      O   25   1.028   0.880   1.221 -0.3017  0.1736 -0.1484

My version of Gromacs is 3.0.5 with single precision.
What could be the problem?

Thanks in advance

Alexander Zuev