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

[Justin A. Lemkul]

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
> 

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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

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