[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Thanks for all your suggestions and help.
The solvation is completed and the system is neutralized.
The position restraint mdrun and final mdrun has worked out successfully
without any warnings and errors this time.
The structure after the final mdrun is not quite acceptable as the lipids
have pulled apart and there is a huge gap between the two layers of the
lipids. I have made the run for 5000 steps with dt = 0.002.
Any suggestions please.

Thanking you,

Yours sincerely,
Pawan

On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> Thanks for all your kind help and suggestions.
>> I will work on this and ask you if I have further doubts.
>> Is it fine if I use the perl code given in
>> wiki.gromacs.org/membrane-simulations <
>> http://wiki.gromacs.org/membrane-simulations> for solvation after the
>> genbox step to remove extra waters from the hydrophobic part of the bilayer
>> ?
>>
>>
> You mean the C program or shell script at
> http://wiki.gromacs.org/index.php/Membrane_Simulations?  Yes, either of
> those should be fine.
>
> -Justin
>
>  Thanking you,
>>
>> Yours sincerely,
>> Pawan
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> 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
>>
>> ========================================
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090406/6c63d8d4/attachment.html>