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

[minnale]

  Thanks for your invaluable reply to Justin and syma.


On Sun, 29 Jun 2008 Justin A.Lemkul wrote :
>
>
>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> 
>> >>
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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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>-- ========================================
>
>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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