Hi Lekpa,
On 5/5/2010, at 2:37 p.m., Lekpa Duukori wrote:
> 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:
> <snip>
>
> When I run wham like:
>
> wham 0.0 180.0 10 0.000001 300.0 3 metafile.dat free.dat
>
> I only get nans
>
> A picture of histogram of part (for clarity) my data is attached.
>
> What could be wrong here?
>
> Thanks for your time!
How are you generating your zeta.dat files, and what does one of them look like? I can't see the name "zeta.dat" in your &wt section.
Ben
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Received on Wed May 05 2010 - 12:00:11 PDT
