[gmx-users] nvt.gro

[ram bio]

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.

Thanks

Ram

On Tue, Sep 22, 2009 at 8:25 PM, ram bio <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> 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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