[gmx-users] Simulation of membrane protein
jmsstarlight at gmail.com
Fri Nov 11 13:08:47 CET 2011
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 ?
2011/11/11 Justin A. Lemkul <jalemkul at vt.edu>
> James Starlight wrote:
>> 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 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
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