[gmx-users] RE: Avoid centering in genbox

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Thu May 31 07:42:26 CEST 2007

FYI, best to keep these sort of discussions on the emailing list.  That
way information is there for others to see and refer to in the future.

>Thanks for replying to the querry.
>My problem is unique, as I am setting up an AFM pulling in one
>If I could keep the solute to one side of the box, there is sufficient
>box length on the other side to pull into. ( because the molecule is
long - a triglyceride) 
>Otherwise if I make it in center,  it would call for additional expense
of computation
>time (because of extra water molecules on one side - not required)

I have no idea about the pull code, but assuming that it does have
issues with the PBC ....

Then after the system has been solvated I would then move the molecule
of interest to the edge of the box.  Do that by centering the box (using
editconf -c) on a water molecule somewhere in the system such that the
centering moves the molecule of interest back to the side.  Suspect that
you pick the water to use by visualing the system after solvation with
something like VMD, select a water molecule on the center of one of the
sides of the cube and try that.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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