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

Reply via email to