Hi, If the position restraints are only on the protein, then the water and lipids are free to move about- assuming you have a cavity in your protein wide enough to accommodate water- then water (or lipids) depending on the nature and location of the cavity, should move in as a vacuum is not energetically favored.
If you wish to place waters in the pore/cavity yourself prior to simulation, there are codes available that can do this (vmd has a plugin i think), you can also use voidoo and flood. I have never used to gromacs to do this- but it is likely someone else has, did you check the archives? Best wishes, -Syma In message <[EMAIL PROTECTED]> minnale <[EMAIL PROTECTED]>, Discussion list for GROMACS users <gmx-users@gromacs.org> writes: > Thanks for your prompt reply, according to you for membrane protein > protocols keep restrain only on protein but not on lipid and water, is there > any possibility to move water inside pore of the membrane when keep restrain > only on protein. > Could you please tell me > Thanks a lot in advance > > > On Sun, 29 Jun 2008 Justin A.Lemkul wrote : > > > > > >minnale wrote: > >> > >> HI users, > >> I have embedded protein in popc bilayer and ran the minimisation > >> succesfully , before going equilibration I would like to confirm one thing > >> that how to run the equilibration with on which system keep position > >> restrain? > >> > >>1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, > >>-DPOSRES_LIPID, -DPOSRES_WATER) at a time ? > >> > >>or 2. keep position resrain on each system at a time and > >> 3.is it require to keep position restrain on water? > >>Could you tell me clearly pls > >>Thanks alot in advance > >> > >> > > > >If you "equilibrate" your system with every element of it restrained, I > >think you will accomplish absolutely nothing. Typical procedures for > >membrane proteins involve equilibrating with restraints on the protein only, > >allowing the lipids to pack around the protein. > >-Justin > > > >> > >>HSBC > >><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL > >> PROTECTED]/2204104_2196511/2199118/1?PARTNER=3&OAS_QUERY=null> > >> > >>------------------------------------------------------------------------ > >> > >>_______________________________________________ > >>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 [EMAIL PROTECTED] > >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > >-- ======================================== > > > >Justin A. Lemkul > >Graduate Research Assistant > >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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
