From: Randy J. Zauhar (r.zauhar_at_usciences.edu)
Date: Mon Oct 07 2013 - 08:50:07 CDT
Hi, I am trying to turn on collective variable restraints in the course of a simulation, as is done in one step of the binding free energy simulation ('alchemical version') described in the "Protein Ligand" tutorial (Gumbart, Roux & Chipot).
The sample restraints files includes entries similar to this, for each collective variable:
lambdaSchedule 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.99 0.999 0.9999 1.0
Apparently this is intended to increase the force constant from 0. to the target 0.1, according to the lambda schedule specified. It appears there should be 50000 steps total for each lambda setting, with data collection for 40000 steps in this case.
1) This lambda schedule is specified individually for every collective variable - how can that be? What if the schedules or number of dynamics steps are not consistent with each other?
2) In the sample namd input file (rest-01.namd) the only action that deviates from a straight dynamics simulation is to turn on the colvars -
- there is no other specification connected to FEP. In fact, in running this, I see no 'special' output connected to the variables or the changing hamiltonian.
So, clearly I am missing a lot here (in fairness to me, that tutorial is also missing a lot!!) I would appreciate any pointers as to what I need to include.
Randy J. Zauhar, PhD
Assoc. Prof. of Biochemistry
Director, Graduate Program in Bioinformatics
Dept. of Chemistry & Biochemistry
University of the Sciences in Philadelphia
600 S. 43rd Street
Philadelphia, PA 19104
"The blunt, pathetic reality today is that a little old lady has died, who in the winter of her life had to water roses alone under police supervision. If you behave like there's no such thing as society, in the end there isn't. "
-- Russell Brand on Margaret Thatcher
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