Respected Sir, Thanks for all your help. I will try this out and if I have any further queries I will ask you. Thanks a lot.
Thanking you, Pawan On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: Pawan Kumar wrote: > Respected Sir, > > Thanks for all your help, suggestions and guidance. > I have few more queries. > Which type of box is appropriate in editconf - cubic or triclinic ? > That depends entirely upon the dimensions of your system and what is adequate to accommodate the size of your embedded protein. I have read in one of your mails in the archives that POPE bilayer contains > some bad interactions. As it contains more no. of lipids (340) it covers the > full protein ( trimer which I am working on ) other than the few loop > regions. How far that bilayer can be used or is it fine to use the biger > bilayer of popc128a whcih I obtained by genconf ? > > The choice of lipid should not be based on a size convenience. It should be based on a valid model system, and experimental evidence to which you can correlate your results, if possible. POPE presented a terrible challenge, since during the in vacuo InflateGRO minimizations, the headgroups folded in on themselves to form intra-molecule hydrogen bonds that resulted in a collapse of the molecule. The solution was to use freeze-grps in all dimensions during these minimizations, and then equilibrate very carefully. >> >> Justin A. Lemkul >> Graduate Research Assistant >> ICTAS Doctoral Scholar >> 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 gmx-users@gromacs.org >> http://www.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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >
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