[gmx-users] About Protein in Bilayer Simulation
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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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