[gmx-users] Simulation of membrane protein

[James Starlight]

Justin,

What temperature for NVT phase should be in

gen_temp    = 323

Does this parameere must be equal to the ref_t ?

I've obtain strange results after NVT with
ref_t   = 297     297    297

for protein in DMPC bilayer.

The bilayer with water parts diffused in up and down direction of the box
relative protein
Why this should occur ? Might I alpy posres for lipid in NVT phase ?

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

>
>
> James Starlight wrote:
>
>> 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 ?
>>
>>
> It is incorrect to set different groups at different temperatures.
>  Whatever result you obtain would be completely unrealistic.
>
> -Justin
>
>
>> James
>>
>> 2011/11/11 Justin A. Lemkul <jalemkul at vt.edu <mailto: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
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> 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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