FEP anomaly?

From: Christopher Hartshorn (cmhartshorn_at_wsu.edu)
Date: Mon Feb 23 2009 - 12:53:15 CST

Hi everyone. After running an FEP calculation (see parameters below
message),I am obtaining an FEP graph (dG vs Lambda step) which seems
odd. I write to this forum because I think it is my system (or
parameters) and not an actual physical result. Essentially I am
seeing, as lambda goes from 0 to 1, the dG drop below zero, hit a
minimum (around -120), and then rises again to around lambda step
0.98. This is what I expect. But at around lambda step 0.98, it
reverts going negative again (e.g it rises from -120 to about -44, at
lambda=0.98, then reverts and ends around -50 at lambda=1). Is this
one of those end point anomalies? Does my config. file seem okay (e.g
using Langevin coupling to pressure/temp baths, etc.)? I'm using a
CVS build from Dec 2, 2008 is this a good build for FEP? etc.

Thank you to all for any help you can offer.

Chris Hartshorn
WSU

structure dmpc_mid1.psf
coordinates mdsim2ns_out.coor
velocities mdsim2ns_out.vel
extendedSystem mdsim2ns_out.xsc
set outputname dmpcmid1FEPGA155ksteps04_out

# firsttimestep 1000000

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input parameters
paraTypeCharmm on
parameters par_all27_prot_lipid_sil.inp
parameters par-extraterms.inp

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 10.0
switching on
switchdist 8.5
pairlistdist 11.5

# Integrator Parameters
timestep 1.0 ;# 1fs/step
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

margin 1

wrapWater on
wrapNearest off

# PME (for full-system periodic electrostatics) only with PBC's
# Must get cell dimensions from PBC basisvectors for accurate PME
# Remember multiples of 2,3, and/or 5
PME on
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 100

# Constant Pressure Control (variable volume) only for PBC's
useGroupPressure yes # smaller fluctuations
useFlexibleCell no # allow dimensions to fluctuate independently

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 10 ;# damping coefficient (gamma) of 10/ps
langevinTemp 310
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Nos´e-Hoover Langevin piston pressure control
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.0
langevinPistonDecay 100.0
langevinPistonTemp 310

rigidbonds all
rigidtolerance 0.000001
rigiditerations 400

fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fixQ011.pdb
fixedAtomsCol B

#############################################################
## EXECUTION SCRIPT ##
#############################################################
# FEP

source fep.tcl

fep on
fepFile dmpc_mid1_FEPGA1.fep
fepCol B
fepOutFile DMPCmid1GA155ksteps04.fepout
fepOutFreq 10

# LOOP OVER LAMBDA-STATES

fepEquilSteps 5000
set nSteps 110000

set dLambda 0.04

set init {0.0 0.00001 0.0001 0.001 0.01 0.02}
set end {0.98 0.99 0.999 0.9999 0.99999 1.0}

runFEPlist $init $nSteps
runFEP 0.02 0.98 $dLambda $nSteps
runFEPlist $end $nSteps

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