<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>dear all gromacs-users ,<br>
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.<br>
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:<br>
Correcting invalid box:<br>
old box (3x3):<br>
old box[ 0]={-9.43863e+07, 0.00000e+00, -0.00000e+00}<br>
old box[ 1]={ 0.00000e+00, -9.43863e+07, -0.00000e+00}<br>
old box[ 2]={ 0.00000e+00, 9.91055e+09, -9.43863e+07}<br>
new box (3x3):<br>
new box[ 0]={-9.43863e+07, 0.00000e+00, -0.00000e+00}<br>
new box[ 1]={ 0.00000e+00, -9.43863e+07, -0.00000e+00}<br>
new box[ 2]={ 0.00000e+00, 1.00049e+10, -9.43863e+07}<br>
<br>
I have no idea what I can do. Please help me out.<br>
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.<br>
<br>
Rahul Karyappa<br>
NCL, India<br>
<br>
<br>
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