[gmx-users] nvt.gro

[Justin A. Lemkul]

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 <rmbio861 at gmail.com 
> <mailto:rmbio861 at 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 <jalemkul at vt.edu
>     <mailto:jalemkul at 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

========================================