restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF?

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sun Oct 19 2008 - 13:43:56 CDT

Dear All,

I am trying to restart a PMF calculation.
The freeEnergy script of my *very first* namd run was:

****************************
freeEnergyConfig {
        urestraint {
                dist pmf group { (A, 11) }
                                group { (A, 210) } kf=20, low=28.37, hi=18.0
        }
        pmf {
                task = grow
                time = 1500 ps
                print = 1 ps
        }
        pmf {
                task = up
                time = 15000 ps
        }}
****************************

For the restart,

****************************
freeEnergyConfig {
        urestraint {
                dist pmf group { (A, 11) }
                                group { (A, 210) } kf=20, low=27.644,
hi=18.0
        }
        pmf {
                task = up
                time = 13950 ps
                print = 1 ps
        }}
****************************

1.) Will this restart actually start at kf=20, or will I need to
introduce a "grow" phase again, so that it doesn't start at kf=0? The
output at step 1000 was lambdaKf=1.0 and lambdaRef=0.00007.

2.) What is "lambdaRef" by the way? Is this only for the logfile, or
does it have a physical meaning - do I need to reset it properly for the
restart, too? If yes, how?

3.) Is there any more documentation about pmf beyond the namd script, so
that I don't have to bug you guys with all these technical questions?

Thank you,
Best,
Sebastian

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