[gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

[Justin A. Lemkul]

minnale wrote:
>
>   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
>

Anything is possible, given the random nature of MD.  It will depend 
largely upon how you prepared your system.  If there is a lot of void 
space around your protein, then water will likely leak in over time, but 
may be forced out by the hydrophobic lipid tails, if you equilibrate 
long enough.  If your lipids are nicely packed around your protein 
(using a method like InflateGRO from Tieleman's site) then this 
occurrence is less likely.

The most important thing to do is to consult the literature regarding 
similar systems and take note of what those authors have done.  How did 
they insert the protein?  How did they equilibrate the system, and for 
how long?

-Justin

>
> 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> 
>
> >>
> >>------------------------------------------------------------------------
> >>
> >>_______________________________________________
> >>gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> >>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 at 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-request at gromacs.org.
> 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

========================================