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 <20080629160000.29790.qmail@f5mail-237-215.rediffmail.com> minnale  <minnale_gnos@rediffmail.com>, 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/1050715198@Middle5/2204104_2196511/2199118/1?PARTNER=3&OAS_QUERY=null> 
> >>
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> >Justin A. Lemkul
> >Graduate Research Assistant
> >Department of Biochemistry
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