[gmx-users] Position Restrained Simulation for Coarse Grained DSPC

[sunny mishra]

Hi,

Thanks a lot for the quick reply. I want to position restrain the head group
atoms of CG DSPC  but I am not sure about the head group molecules in DSPC.
Can you please tell me how to figure out the head group atoms or molecules.
Also, when you say co-ordinate file then you mean .itp file for the lipid
right?

Thanks

On Wed, Jun 23, 2010 at 2:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> sunny mishra wrote:
>
>> Dear All,
>>
>> I am trying to run the Position Restrained simulation for the Coarse
>> Grained DSPC bi-layer. However, I am quite confused that how to generate the
>> position restraint file for the CG atoms in lipid. Is there a difference
>> between the position restraint file for the fine grained and coarse grained
>> structures. Please let me know how to generate the position restraint file
>> for Coarse Grained DSPC bi-layer. Your reply for the same will be highly
>> appreciable.
>>
>
> You can generate a position restraint file for any molecule using genrestr.
> Just make sure to supply it with a coordinate file for a single molecule
> (i.e., not your entire bilayer), since position restraints are applied to
> moleculetypes, and not global structures.
>
> -Justin
>
>
>> Thanks,
>>
>> Sunny
>>
>>
> --
> ========================================
>
> 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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