[gmx-users] About Protein in Bilayer Simulation

[Justin Lemkul]

On 10/5/12 10:39 AM, vidhya sankar wrote:
> Thank you Justin For  Your Previous reply
>
> Finally Somehow I have  Adjusted  The Cut-Off  and  Grid Size and Inserted Protein in Lipid By Deleting some Lipid Molecules  MY Question is
>
>                                                               1)  When I am Using inflategro  Perl  Script ,I need to Use Cut-off , Scaling Factor ,Grid size ,
>
> Is there is Any Rule to Set up Suitable Factor (Aforesaid)  For my System ?
>

Please read the paper associated with the InflateGRO script.

> 2)  I need to Use Only  Protein Surrounded By Lipid Molecules . I Do not Want to use  genion tool to insert water .
>
> Is it Possible ?  and  Is it Reasonable  To do Direct Minimization, Equilibration, Production MD  without Water ?
>

You can do EM without water, but trying to simulate a protein in a membrane in 
vacuum does not make sense.  The force fields are not designed to be used in 
this way.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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