[gmx-users] nvt.gro
ram bio
rmbio861 at gmail.com
Mon Sep 28 14:44:07 CEST 2009
Dear Justin,
When I used the energy mininized system for NPT annealing with position
restraints on lipids and there was no separation. So, I think I can proceed
now to equiliration phase 2 (1-ns NPT equilibration-NPT) and then run the
Molecular Dynamics for data collection(1ns).What do you suggest, is it the
right way i am following..as i will be not be using NVT equillibration
anywhere through out the process.
Thanks,
Ram
On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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