[gmx-users] Simulation of membrane protein

[James Starlight]

Thanks Justin

I'll try to do that things.

Some addition questions

1) About nvt and apt equilibration

As I understood ref_t of the system  must be equal to temperature of the
phase transition of the specific LIPID.
But in the npt and nvt.mdp files there are severl enties for ref_t ( for
some system groups in index.ndx )
For my system composed of protein dmpc and water :

    ref_t   = 323     297    323            ;

Does all this values in mdp file must be equal ( to the temperature of the
lipid  phase transition)
ref_t   = 297     297    297

 or each value must correspond to the temperature of phase transition of
the individual element ?
    ref_t   = 323     297    323            ;

Does thic correct for both NPT and NVT ensembles ?


James

2011/11/11 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>> Justin,
>>
>> Could you tell me what difference in inflategro parameters ( cut-off for
>> lipid removing and scaling factors) should I make for insertion protein in
>> another bilayes in comparison tu tutorial ?
>>
>>
> I've never made any changes; it's always worked just fine.
>
>
>  Now I'm working with DMPC. I've inserted symmetrical alpha helices
>> protein in this bilayer but inflategro deleate 2 lipid from upper and just
>> 1  from lower layer. It's strange because I suppose that equal bilayer
>> molecules would be removed :o
>>
>>
> The number of lipids that are removed will depend on the starting
> configuration of the membrane and thus where lipids are relative to the
> protein. Theoretically, a symmetrical protein should delete an equal number
> of lipids from each leaflet, if the geometry of the top and bottom leaflets
> is comparable.  Either try placing the protein at a different location to
> achieve equivalent removal or manually delete a lipid and be sure to
> equilibrate adequately.
>
>
>
>> On Inflategro's sites I havenot found such specifity for above parameters
>> for different bilayers :(
>>
>
> The cutoffs specified are simple grid search parameters.  They do not
> necessarily need to be altered depending upon the lipid type.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
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> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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