[gmx-users] error while running mdrun

[Rahul Karyappa]

dear all gromacs-users ,

       This is very important for me. I
really need your help to solve this problem. I have to run MD on a 48
repeat units polymer surrounded by water molecules in a box. For a test
run I have taken MD parameters which are given on the GROMACS website
under .mdp file format option.

      When I ran the mdrun, it starts but as
time progresses the size of the md.log file keep increasing with the
errors. One error type is like as follows:

Correcting invalid box:

old box (3x3):

   old box[    0]={-9.43863e+07,  0.00000e+00, -0.00000e+00}

   old box[    1]={ 0.00000e+00, -9.43863e+07, -0.00000e+00}

   old box[    2]={ 0.00000e+00,  9.91055e+09, -9.43863e+07}

new box (3x3):

   new box[    0]={-9.43863e+07,  0.00000e+00, -0.00000e+00}

   new box[    1]={ 0.00000e+00, -9.43863e+07, -0.00000e+00}

   new box[    2]={ 0.00000e+00,  1.00049e+10, -9.43863e+07}


I have no idea what I can do. Please help me out.

One more thing, when I ran mdrun for smaller no. of repeat units like
1,2 and 4 it ran successfully. Looking forward to your kind reply.
Thanking you in advance.


Rahul Karyappa

NCL, India






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