[gmx-users] nvt.gro
Justin A. Lemkul
jalemkul at vt.edu
Fri Sep 25 19:53:25 CEST 2009
ram bio wrote:
> Dear Justin,
>
> As suggested, i increased the force constant in the Z dimension from
> 1000 to 10000, and did the NVT equillibration, but still the gap
> existed, then i gave the output of nvt equillibration that is nvt.gro as
> input for the NPT anneling simulation (suggested as with position
> constraints, 1000) and simulated and here also i had gap .between layers
> when npt.gro was viewed in VMD.
>
> I have a query that is can I use nvt equllibrated system as input for
> NPT simualated annealing or should I use the initial ionized and
> minimized system for the NPT annaelated simulation, as the gap is still
> persisting...
>
Use the energy-minimized system as the input into annealing. I have no idea why
this separation would be happening in this system, unless the box has been
prepared improperly. I chose the KALP-DPPC system because it is very robust in
everything we've tried to subject it to.
-Justin
> Thanks
>
> Ram
>
> On Thu, Sep 24, 2009 at 4:16 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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> <mailto: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>
> <mailto: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> <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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
--
========================================
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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