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

[minnale]

  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
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
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