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

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