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<P>Dear all:</P>
<P> </P>
<P>In my previous message "Mdrun interrupted using a triclinc box", I mentioned
that my mdrun would be crashed after ~200ps. </P>
<P> </P>
<P>After kind help and suggestion by Dr. Tsjerk, I firstly had a look at md.log,
and the following abnormal things were listed in the last lines:</P>
<P> </P>
<P>Large VCM(group rest):
0.00804, 0.00429,
0.01242, ekin-cm: 3.77926e+01<BR>Large VCM(group rest):
512956500541440.00000, 245353177677824.00000, -548765085728768.00000,
ekin-cm: 9.94896e+34</P>
<P> </P>
<P>Then, I located the relative answers in mailing list, and it seems that the
problem should be atrributed to the removal of center-of-mass velocity. In my
current simulation, I removed the center-of-mass translocation of <STRONG>the
whole system</STRONG> every step by setting "comm-mode = Linear" & "nstcomm
= 1". </P>
<P> </P>
<P>Because in my system, several protein chains are included. So, Did I need to
make C.O.M removal for every seperated group? For example, is it ok for me to
define "comm_grps = Protein1 Protein2 Protein3"?</P>
<P> </P>
<P>Thanks in advance.</P>
<P> </P>
<P> </P>
<P>Xie Yinghong</P>
<P>Hong Kong Univ.</P></BODY></HTML>