[gmx-users] About Protein in Bilayer Simulation

Justin Lemkul jalemkul at vt.edu
Fri Oct 5 16:42:17 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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