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>>
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>>>
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://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
==============================____==========
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>>
Please search the archive at
http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>
<http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search>> before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read
http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>
<http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>>
--
==============================__==========
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>
==============================__==========
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
