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.
best
Albert
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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