VMD-L Mailing List
From: Raul Araya Secchi (arayasecchi_at_hotmail.com)
Date: Fri Mar 24 2006 - 10:49:09 CST
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Hi, NAMD users....
Still working with som FEP calculations and I have the following questions:
If one put the MINIMIZE comand in the following way
while {$step >= 0.1 && $step < 0.9} {
lambda $step
set step [expr $step+$dstep2]
lambda2 $step
minimize 1000
run 150000
lambda $step
set step [expr $step+$dstep2]
lambda2 $step
minimize 1000
run 150000
does this minimization goes acording to lambda or is a minimization of the dual topology hibrid without recongnizing which atoms appear or dissapear? I mean, does the minimize command minimize each lambda state during the FEP or not?
And in other matter....does anyone have made Overlap Sampling - FEP ??
I`ve read the papers about it but I have some quiestions and doubts on how to really do it with NAMD...so any hel will be apreciated
Thanks
Good Luck for all
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- Next message: John Stone: "Re: Possible error in aligning/computing RMSD of 2 molecules with three or two atoms"
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