Respected Sir, Thanks for your help and suggestions. First I will try to use POPC (the one generated using genconf) . If it doesnt work then I will switch over to POPE. I will ask you if I have any further queries.
Thanking you, Pawan On Mon, Mar 23, 2009 at 6:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Pawan Kumar wrote: > >> >> 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 ? >> >> > If you search for "freezegrps" within the list archive (the "Search" > feature of the Gromacs homepage), you will find several hundred results, > many of which provide examples of what users are trying and what may or may > not work. This should be instructive. > > In a general sense, freezegrps are just like anything else under the group > theory in Gromacs. Make an index group for the group of atoms you want to > freeze (i.e., headgroups) and the dimensions in which you want them frozen > (x, y, z - yes(Y) or no(N) for each). > > If you are choosing the route of POPE, it is very difficult to get these > systems built using InflateGRO. At least, that has been my experience. > Prepare to spend a lot of time with trial and error and very careful > equilibration. > > -Justin > > Thanking you, >> Pawan >> >> On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul <jalem...@vt.edu >> <mailto: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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> > -- > ======================================== > > > 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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