Date: Wed, 5 May 2010 12:37:15 -0600
Hi Everyone,
I am having some problems with WHAM analysis after umbrella sampling. I am
using the WHAM code from the Grossfield lab.
I did umbrella sampling with input files like the following in windows of 10
degrees ( for an improper dihedral: from 180 to 0 ):
Restart file is from an approx 10ns NPT calculation
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 1,
cut = 8,
ntc = 2,
ntf = 2,
temp0 = 300.0,
ntt = 3,
nmropt=1,
gamma_ln = 1.0,ig = -1,gamma_ln = 3.0,
nstlim = 3000000, dt = 0.001
ntpr = 100, ntwx = 100, ntwr = 1000
/
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG=dihedral.11.RST
LISTIN=POUT
LISTOUT=POUT
DUMPAVE=dihedral.11.out
dihedral.11.RST file:
&rst iat=2,6,8,18 r1=-10, r2=90, r3=90, r4=190, rk2=100., rk3=100., /
my metadata file for the wham code is like this:
umbrella.02/zeta.dat 180.0 200.0
umbrella.03/zeta.dat 170.0 200.0
umbrella.04/zeta.dat 160.0 200.0
umbrella.05/zeta.dat 150.0 200.0
umbrella.06/zeta.dat 140.0 200.0
umbrella.07/zeta.dat 130.0 200.0
umbrella.08/zeta.dat 120.0 200.0
umbrella.09/zeta.dat 110.0 200.0
umbrella.10/zeta.dat 100.0 200.0
umbrella.11/zeta.dat 90.0 200.0
umbrella.12/zeta.dat 80.0 200.0
umbrella.13/zeta.dat 70.0 200.0
umbrella.14/zeta.dat 60.0 200.0
umbrella.15/zeta.dat 50.0 200.0
umbrella.16/zeta.dat 40.0 200.0
umbrella.17/zeta.dat 30.0 200.0
umbrella.18/zeta.dat 20.0 200.0
umbrella.19/zeta.dat 10.0 200.0
umbrella.20/zeta.dat 0.0 200.0
When I run wham like:
wham 0.0 180.0 10 0.000001 300.0 3 metafile.dat free.dat
I only get nans
#Number of windows = 19
# Dumping simulation biases, in the metadata file order
# Window F (free energy units)
# 0 nan
# 1 nan
# 2 nan
# 3 nan
# 4 nan
# 5 nan
# 6 nan
# 7 nan
# 8 nan
# 9 nan
# 10 nan
# 11 nan
# 12 nan
# 13 nan
# 14 nan
# 15 nan
# 16 nan
# 17 nan
# 18 nan
# No MC error analysis requested
A picture of histogram of part (for clarity) my data is attached.
What could be wrong here?
Thanks for your time!
Lekpa
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