[gmx-users] a question about energygrps

[Albert]

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


do you have any idea why did he use different groups for above paramters 
in NVT.mdp?

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
>