Hello Ben,
My zeta.dat files was generated by ptraj
It looks like this
timestep dihedral
5001.00 61.634403
5002.00 73.807835
5003.00 68.285963
5004.00 69.185732
5005.00 77.925740
5006.00 67.384091
5007.00 67.790124
5008.00 68.074948
5009.00 62.289917
5010.00 65.399225
One is attached ( for r2=r3=70 degrees)
Thanks
Lekpa
On Wed, May 5, 2010 at 12:45 PM, Ben Roberts <roberts.qtp.ufl.edu> wrote:
> 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 - 13:00:03 PDT
