[gmx-users] frozen group, pull code and COM motion removal

[Allen Smith]

In message <46E42EE4.2040705 at xray.bmc.uu.se> (on 9 September 2007 19:35:32
+0200), spoel at xray.bmc.uu.se (David van der Spoel) wrote:
>[someone] wrote:
>> Hi all,
>> 
>> Recently, I performed a simulation which have three groups: frozen group 
>> (there's no connections with the other groups), free group (peptide), 
>> mobile group (using AFM pulling of the pull code) . How should I set the 
>> comm._mode and comm _grps in the mdp file?
>> 
>more info please.

I believe at least part of the question is whether a frozen group will be
moved at all by the COM motion removal (e.g., if rotation of the rest of the
system to cancel out center-of-mass motion might do something like leaving
the frozen part behind).

      -Allen

-- 
Allen Smith			         http://cesario.rutgers.edu/easmith/
There is only one sound argument for democracy, and that is the argument
that it is a crime for any man to hold himself out as better than other men,
and, above all, a most heinous offense for him to prove it. - H. L. Mencken