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 <jalem...@vt.edu <mailto:jalem...@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 <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@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 <jalem...@vt.edu
<mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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
-- ==============================______==========
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