[gmx-users] About Protein in Bilayer Simulation

vidhya sankar scvsankar_agr at yahoo.com
Fri Oct 5 16:39:50 CEST 2012

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 ?

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 ?

Thanks In Advance 

S.Vidhya sankar
With Regards 

S.Vidhya sankar

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