[gmx-users] nvt.gro
ram bio
rmbio861 at gmail.com
Mon Sep 28 18:37:47 CEST 2009
Dear Justin,
Thanks for the options and suggestions, will be back after some trials with
modelled proteins.
Ram
On Mon, Sep 28, 2009 at 6:17 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>
>> 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.
>>
>>
> I think that should be fine. There is really no prescribed way to do
> equilibration, necessarily. Everyone has their own method. If you can
> stabilize the temperature and pressure prior to data collection, then you've
> done enough, in general. Just be aware that my definition of "data
> collection" simply means that you're remove restraints from anything that
> was previously restrained. Collecting data for membrane protein systems
> often occurs after 10-20 ns (or more), to allow for re-orientation of
> lipids, which is very slow.
>
> -Justin
>
> Thanks,
>>
>> Ram
>>
>>
>> On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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>
>> <mailto: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>>
>> <mailto: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>>
>> <mailto: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>
>> <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> <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 <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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