[gmx-users] error comm-grps=Protein SOL

M. Emal Alekozai memala at gmx.net
Fri Aug 8 00:44:09 CEST 2008


 >>2. If the option "comm-grps = Protein SOL" physical means (1b) what do
 >>I have to change in my simulation setup to avoid the warnings/ error 
 >>"T-cm: inf" in the log files?
 >comm-grps = System (as you noted, it does not give the error!)

I forgot to mention that my system contains except the group "Protein" 
and "SOL" also other groups/ atoms.
If I would select "System" all the atoms would be considered in the 
center of mass calculation and not only the atoms of the group "Protein" 
and "SOL" :-( .

There is a large set of old short trajectories which where simulated 
with the settings "comm-grps = Protein SOL".
I want to create a longer trajectory with the same settings and compare 
it with the old short trajectories.
If I use in the new long simulation the setting "comm-grps = System" I 
would most likely get a different physical system. The comparison of the 
old short trajectories and the new long trajectory would most ilkley be 
biased because of the different parameters.

I can't use for the long simulation the settings "comm-grps = Protein 
SOL" because the log files would fill up my harddisk before the 
simulation really starts.

Any help to solve this dilemma is welcome :-) .

Thanks Emal

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