[gmx-users] About DPPC Cut-off

Justin Lemkul jalemkul at vt.edu
Sun Oct 28 17:16:35 CET 2012

On 10/28/12 12:01 PM, vidhya sankar wrote:
> Dear justin Thank you for your previous reply,
>                                                                              Finally I Have Found out problem When I Shrink My system Using Script The Size of the box at the end of System_inflated.gro file is not as i Have Assigned previously   it has been Changed From Box size from 6 6 6 to    27   27   6.00  when I edit The end line of  Output file Everything become Ok (when i Solvate it has been solvated with 1024 sol Molecules)

You should not manually change the box vectors.  The whole point of InflateGRO 
is to expand and compress the system.  Leave the box vectors it assigns alone.

> Now Can i use different  DPPC Cut-off Value (20 or 25 )  ?  or Different Scaling Factors (instead 0.95)

Larger cutoffs lead to greater numbers of lipids being deleted and thus extends 
the time it takes to compress the system back.  The value of 14 suggested by the 
authors of the script has always worked for me.

> Because When i Use 14  for my System No Lipid Molecules has been Deleted

That's certainly unusual.

> Also There is sudden Shrink in APL When I go from first iteration and EM  to Second Shrink  ( from  93A to 4.7A)
> Why Such Drastic Fall of APL Occurs?

Without seeing your commands and the actual screen output, I can't comment, but 
I find this highly unlikely.

> How to Rectify this Problem?

No clue.  Very little of what you are saying makes any sense to me.



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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