[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 :-) .
More information about the gromacs.org_gmx-users