[gmx-users] Simulation of membrane protein
James Starlight
jmsstarlight at gmail.com
Fri Nov 11 18:32:34 CET 2011
Justin,
It was a huge bilayer replacement on the magnitude comparable with the
protein size. In more detailes both of the lipid leflets moved to the top
and bottom side of the pb. The protein were placed on the old place ( due
to the posres) so it turned out isolated from membrane :)
Also I've found that I could use simulated annealing to slowly warm the
system under *NPT* conditions
So in this case could I skip the nvt phase and do this mod NPT
equilibration ?
also I've create posres for the lipid on Z direction only. I hopes this
helps prevent such bilayer diffusion.
James
2011/11/11 Justin A. Lemkul <jalemkul at vt.edu>
>
>
> James Starlight wrote:
>
>> 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.
>>
>>
> You should generate velocities for the temperature you wish to use.
> Otherwise, equilibration will take longer than necessary. At worst, it
> may crash if your system is far from equilibrium as the temperature
> coupling algorithm may fail.
>
>
> 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 ?
>>
>>
> Given that I know nothing about the magnitude of such motion, I can't
> really say. If there are severe distortions or displacements, restraining
> headgroup atoms may be necessary for the initial phases of equilibration.
> Usually such restraints should not be necessary for most well-built
> systems.
>
> -Justin
>
> 2011/11/11 Justin A. Lemkul <jalemkul at vt.edu <mailto: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> <mailto: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> <http://vt.edu> | (540)
>> 231-9080
>> http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>> <http://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<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 <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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