ram bio wrote:
Dear Justin,
As suggested in the tutorial by you i applied the lipid position
restraints, while running the NVT equillibration, but after the job is
finished, when i observed the nvt.gro file in VMD, still there is a gap
between the lipid bilayers but this time the gap is not so large as it
was in the earlier run (as discussed earlier in previous email).
As I was already running the NPT equillibration(which I obtained after
the earlier NVT job, which ended in large gap between layers), i just
wanted to observe it and here there is no gap in between the layers i.e.
in npt.gro.
Please suggest me what to do to lower the gap after NVT equillibration
even after applying the lipid restraints and is it ok for my NPT
equillibration as there are no gaps between the layers after this NPT
equillibration.
The gap arises because the lipids (when free to move) are attracted to the water
above and below the bilayer. If the protein is restrained, it doesn't move.
The box size in NVT is fixed, so the system is trying to fill it. It could be
that your box was inappropriately assigned (too large), but maybe not.
I am surprised that, even when using position restraints, the lipids still
separated at all. Did you use the lipid_posre.itp file that I provide on the
tutorial site? It has always worked well for me in such cases. You could also
try increasing the force constant in the z-dimension.
The other option is to do NPT simulated annealing, as I also suggest in the
troubleshooting page. Using NPT allows the box to deform in response to the
system, so you will probably get less weird behavior. I have found that both
NVT with PR and simulated annealing can get the job done.
-Justin
Thanks
Ram
On Tue, Sep 22, 2009 at 8:25 PM, ram bio <rmbio...@gmail.com
<mailto:rmbio...@gmail.com>> wrote:
Dear Justin,
Thanks for the suggestion, will try to apply position restraints on
lipid as mentioned in the advanced trouble shooting section.
Ram
On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
ram bio wrote:
Dear Gromacs Users,
I am following the justin tutorial on KALP-15 in lipid
bilayer, I have a query regarding the nvt.gro that is after
the NVT equillibration phase. The mdrun was proper without
any warnings or errors, but when i visuallized the nvt.gro
in VMD, i found that the peptide is intact in between the
bilayers, but the the two layers got separated or else it is
like the peptide bridging the the two halves of the lipid
bilayer with gap in between the layers and also found few
water molecules to the sides of the peptide or in the gap
mentioned betwwn the layers.
Please let me know is the simulation going on normally or
there is an defect or wrong going on, as the nvt
equillibration was proper as i think i continued for the
next equillibration that is npt for 1ns.
You shouldn't continue blindly if you get weird results. Please
see the "Advanced Troubleshooting" page (part of the tutorial!),
because I specifically address the issue of a bilayer separating:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html
-Justin
Ram
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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