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 <jalem...@vt.edu <mailto:jalem...@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
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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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