[gmx-users] Position restrain of protein and membrane

[minnale]

Thanks Justin for your reply,
You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids?
Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of badcontacts, for that require to keep PR on POPC, so it can relieve badcontacts and get minimised structure. am I right? 
 
On Tue, 16 Sep 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>  Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this?
>
>You could, but I don't see the point.  In equilibrating membrane protein systems, it is very important to optimize the lipid positions around the protein at the outset of the simulation (i.e., packing).  So allowing the protein to move unrestrained while restraining the lipids makes no sense (and you will probably generate some artificial interactions).  You will want to apply PR to the protein, allowing the lipids to pack around it, then remove the PR from the protein and proceed with data collection.
>
>-Justin
>
>>Thanks in advance.
>>
>>On Tue, 16 Sep 2008 Justin A.Lemkul wrote :
>>  >
>>  >
>>  >minnale wrote:
>>  >>Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem.
>>  >>Can you give me suggestion
>>  >
>>  >You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols.
>>  >
>>  >-Justin
>>  >
>>  >>Thanks in advance.
>>  >>
>>  >>
>>  >>
>>  >>
>>  >>  >minnale wrote:
>>  >>  >>  Hi all,
>>  >>  >>I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please.
>>  >>  >>Thank you.
>>  >>  >
>>  >>  >Use "define = -DPOSRES" which is specified in the .top from parameterizing the protein under pdb2gmx.  There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway.
>>  >>  >
>>  >>  >-Justin
>>  >>  >
>>  >>  >>
>>  >>  >>
>>  >>  >>
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>>  >>  >>
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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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>-- ========================================
>
>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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