[gmx-users] a question about energygrps

Albert mailmd2011 at gmail.com
Wed Apr 25 16:49:14 CEST 2012

hello Justin:

   thank you very much for your such kind explanations. It is quite helpful.

   I am wondering how many CPU did you usually use for the membrane 
simulations? and how many ns/day can you get the best if CPU is not a 
problem with Gromacs? I am very confused about this question since some 
one claimed that they can use optimized PMF/F paramters to achieve even 
100ns/day for 20,000 atoms system. I also try to use g_tune_pme to get a 
better performance, but the results are not so satisfied...... Can you 
give me some advices for this?

thank you very much.


On 04/25/2012 04:34 PM, Justin A. Lemkul wrote:
> Indeed I do - I wrote it ;)
> Ideally, one would like to use a single thermostat for the whole 
> system, but in practice, especially for heterogeneous systems, the 
> heat exchange between different groups can be different.  Hence the 
> protein, lipids, and aqueous solvent are coupled separately.  They are 
> of sufficient size to justify their own group (note, for instance, 
> that ions are not coupled separately).
> With respect to the comm-grps, since the system is basically an 
> interface, the lipids and aqueous layers can slide with respect to one 
> another, generating no net COM motion, but each layer may actually be 
> have a net velocity, which would lead to artifacts.
> -Justin 

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