Respected Sir, Greetings from Pawan. I read in the manual about the freeze-grps but dint find a good explanation about the usage. Can you please tell me how to use freeze-grps in all dimensions during the minimizations ?
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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