On 4/25/12 10:20 AM, Albert wrote:
hello Justin:
thank you very much for kind reply.
In gromacs tutorial I found that the author use the following paramters:
tc-grps = Protein DPPC SOL_CL ; three coupling groups - more accurate
comm-grps = Protein_DPPC SOL_CL
OK, just so we're clear: tc-grps, comm-grps, and energygrps are all wildly
different concepts, so don't get them confused.
do you have any idea why did he use different groups for above paramters in
NVT.mdp?
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
thank you very much
On 04/25/2012 04:13 PM, Justin A. Lemkul wrote:
On 4/25/12 10:07 AM, Albert wrote:
Hello:
I am running a membrane simulation with gromacs and I wondering how to deal with
energygrps? Should I put protein and lipids into one energygrps? Or I should
leave the lipids stay with solvent and ions?
You can divide the system in any way you like for energygrps; it's just a
decomposition of the nonbonded terms. The way your break it down depends on
what you care to measure in the system.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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