[gmx-users] nvt.gro

[ram bio]

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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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