[gmx-users] How to Run Energy Minimisation

[Nancy]

Hello,

More specifically, I am unsure as to the procedure of inflating and
minimizing a bilayer using "InflateGRO".  In the tutorial at:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

I followed it successfully up to the inflation step, but I do not know
specifically what parameters to run the energy minimisation.  Please advise.

Thank you.

Nancy




On Wed, Jul 29, 2009 at 7:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Nancy wrote:
>
>> Hello,
>>
>> I am trying to run energy minimisation on a lipid bilayer (downloaded
>> from: http://moose.bio.ucalgary.ca/files/dppc128.pdb).  I inflated the
>> bilayer using "InflateGRO" however, when I try to run the minimisation, it
>> seems to display the un-inflated bilayer.  Please advise.
>>
>>
> Without seeing the command lines that you're issuing, we can only assume
> you are doing something wrong.
>
> -Justin
>
>  Thank you.
>>
>> Nancy
>>
>>
>> ------------------------------------------------------------------------
>>
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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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