[gmx-users] Simulation of membrane protein
Justin A. Lemkul
jalemkul at vt.edu
Fri Nov 11 19:28:20 CET 2011
James Starlight wrote:
> 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 :)
>
>
If the bilayer is splitting across periodic boundaries (I'm assuming that's what
you mean by "pb"), then it's more likely that you placed the components of your
system in an inconvenient way than it is that something is actually wrong.
> 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 ?
>
Prepare the system in whatever manner is defensible and sensible. Normally one
deals with temperature before pressure for stability issues. If you have found
a justifiable protocol that leads to a stable simulation, use it.
-Justin
>
> 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 <mailto: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> <mailto: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>>
> <mailto: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>
> <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://vt.edu/Pages/Personal/justin>>
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>
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> <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> <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 <http://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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--
========================================
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
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