[gmx-users] Large VCM and mdrun crashed
xieyh at hkusua.hku.hk
Wed Oct 12 22:10:32 CEST 2005
In my previous message "Mdrun interrupted using a triclinc box", I mentioned that my mdrun would be crashed after ~200ps.
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:
Large VCM(group rest): 0.00804, 0.00429, 0.01242, ekin-cm: 3.77926e+01
Large VCM(group rest): 512956500541440.00000, 245353177677824.00000, -548765085728768.00000, ekin-cm: 9.94896e+34
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 the whole system every step by setting "comm-mode = Linear" & "nstcomm = 1".
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"?
Thanks in advance.
Hong Kong Univ.
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