questions regrading ABF

From: Jan Saam (saam_at_charite.de)
Date: Mon May 29 2006 - 10:47:48 CDT

Dear fellow NAMDers,

I'm seeking your help regarding a PMF calculation in NAMD using ABF. I
encountered some problems when I tried to do the decalanin unfolding
example from the users guide:

I prepared a decalanin helix, minimized it and then started an ABF
calculation with the parameters from the ABF section of the NAMD user
guide.
My understanding of the method is that a force along the direction of
the reaction coordinate is exerted on the system. The strength of the
force is chosen so that the effect of the (estimated) PMF
preventing the system to travel along the reaction coordinate is
compensated. Thus the uniform sampling over the entire reaction
coordinate is achieved. Correct?

However, no matter how long I run the simulations, only the shorter
distances (18-23 A) were sampled. This behaviour is completely
independent of the abf parameters like the bin size or the smoothing
window size. The helix is immediately unfolded but remains in a globular
state until the end.
It was my understanding that I don't have to use the 'moveBoundary'
option in this example since the adaptive force should take care for the
sampling of the complete reaction coordinate.
Nevertheless, only when I'm using 'moveBoundary' I get resonably uniform
sampling.

Is there anybody who can give me some advice or even send me some
example input?
(I attached the NAMD input file and the abf output file.)

Thanks and best wishes from Berlin,

Jan

-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de


# NAMD CONFIGURATION FILE FOR DECALANIN

# initial config
coordinates alanin_min.coor

# output params
outputname alanin_abf
binaryoutput no
outputEnergies 100

# integrator params
timestep 1.0

# force field params
structure alanin.psf
paraTypeCharmm on
parameters /projects/namd/toppar/par_all27_prot_lipid.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
stepspercycle 20

# trajectories
DCDfile alanin_abf.dcd
DCDfreq 100

# Temperature control
set temperature 310
temperature $temperature; # initial temperature

# Langevin Dynamics
langevin on; # do langevin dynamics
langevinDamping 5; # damping coefficient (gamma) of 5/ps
langevinTemp $temperature; # bath temperature
langevinHydrogen no; # don't couple langevin bath to hydrogens
seed 12345

source /usr/local/NAMD_2.6b1_Linux-i686/lib/init.tcl
package require abf

abf coordinate distance

abf abf1 4
abf abf2 117

abf dxi 0.5
abf xiMin 18.0
abf xiMax 32.0
abf outFile deca-alanine.dat
abf fullSamples 500
abf inFiles {}
abf distFile deca-alanine.dist
abf dSmooth 1.0
abf applyBias yes
abf historyFile deca-alanine.history
run 5000000

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