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 <[email protected]> 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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