FEP + MCTI in one MD simulation

From: List (zheng042003_at_yahoo.com)
Date: Thu Mar 13 2008 - 16:25:36 CDT

Dear NAMD experts,

I would like to do FEP (Free Energy perturbation), at the same time applying thermodynamic integration (MCTI). I have the specifications shown below for FEP and MCTI in the configuration file, about which I'm not sure if the format is correct. It will be greatly appreciated If somebody could tell me if it's in the right format, or correct me if it's not.

###########################################
# FEP PARAMETERS
# equilibrate the system by 40,000 MD steps prior to 160,000 steps of data collection. Total 100 ps of MD sampling
        source ./fep.tcl
        fep on
        fepFile fix.fep
        fepCol B
        fepOutFile fep0t5.fepout
        fepOutFreq 100
        fepEquilSteps 40000
        set nSteps 200000
        set dLambda 0.1

        # windows get narrower to accelerate the convergence of the FEP average
        set init { 0.0000001 0.000001 0.00001 0.0001 0.001 0.01 0.05 0.1 }
        set end { 0.4 0.45 0.49 0.499 0.4999 0.49999 0.499999 0.4999999 }
        runFEPlist $init $nSteps
        runFEP 0.1 0.4 $dLambda $nSteps
        runFEPlist $end $nSteps

        # Thermodynamics integration
        mcti {
           task = stepup
           equiltime = 20 ps # equilibrate for 20 ps at each step
           accumtime = 80 ps # collect dU/d_lambda for another 80 ps
           numsteps = 5 # Number of steps for the change: 0.0->0.1, 0.2
           print = 1 ps
        }

        # reverse the step above (lambda changes from 1->0)
        mcti {
           task = stepdown
        }

#########################################

Regards,

LIST

       
---------------------------------
Never miss a thing. Make Yahoo your homepage.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:19 CST