[gmx-users] Large VCM and mdrun crashed

[leafyoung81-group at yahoo.com]

--- Yinghong <xieyh at hkusua.hku.hk> wrote:

> Dear all:
> 
> 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
Setting separated COM removal group may not work. This
problem is complex and related to un-equilibrated
system. Try to equilibrate more (with high
temperature, position restrained MD). It could be also
related to your force field and topology. Check them
again.

> 
> 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.
> 
> 
> Xie Yinghong
> Hong Kong Univ.
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