Hi Rahul,<br>
<br>
That's a rather large box, measuring millimeters! And the vectors have
negative signs on the diagonal elements, which is weird. Isn't
your system exploding? I'd say something terribly wrong, but can't
comment further without more information (grompp warnings?, energy
minimization?).<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 8/31/05, <b class="gmail_sendername">Rahul Karyappa</b> <<a href="mailto:r.karyappa@ncl.res.in">r.karyappa@ncl.res.in</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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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