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

[Justin A. Lemkul]

sunny mishra wrote:
> 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 

Presumably there is a structure of DSPC somewhere you can refer to.  I would 
think you should know the chemical features of the structures they are 
simulating before diving right in blindly :)

> or molecules. Also, when you say co-ordinate file then you mean .itp 
> file for the lipid right?

No, I mean coordinate file.  An .itp is a topology.

-Justin

> 
> Thanks
> 
> On Wed, Jun 23, 2010 at 2:47 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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-- 
========================================

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

========================================