[gmx-users] nvt.gro
Pramod Akula
ab.pramod at gmail.com
Thu Sep 24 13:06:56 CEST 2009
Dear Justin,
Thanks, will try the options described.
Ram
On Thu, Sep 24, 2009 at 4:16 PM, Justin A. Lemkul <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>> 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
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search
>> before posting!
>> Please don't post (un)subscribe requests to the list. Use
>> the www interface or send it to
>> gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>>
>>
>> -- ========================================
>>
>> 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>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search
>> before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
> --
> ========================================
>
> 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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090924/c07d1fd1/attachment.html>
More information about the gromacs.org_gmx-users
mailing list