[gmx-users] problem in md of methanol box

[刘 松柏]

hi, everyone. I met a problem when I tried to run equilibrated md of 
methanol box which was generated from spc216.gro by replacing one hydrogen 
by CH3, adjusting density to 790 and subsequent em. The .mdp file for md is 
the water.mdp released by gromacs. The following warning jumped out as md 
was running.  I don't what's wrong.

Thanks for any opinion!


Warning: Only triclinic boxes with the first vector parallel to the x-axis 
and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis 
and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis 
and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.




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