Dear SIr,
I tried with three different windows. When I use the makeANG_RST, the
values it generated for rk2=rk3=2.0. I doubled this value and submitted it
to WHAM. But still the output is what it is earlier. It looks like this:
Coor Free +/- Prob +/-
101.000000 nan nan nan nan
103.000000 nan nan nan nan
105.000000 nan nan nan nan
107.000000 nan nan nan nan
109.000000 nan nan nan nan
111.000000 inf nan nan nan
113.000000 inf nan nan nan
115.000000 inf nan nan nan
117.000000 inf nan nan nan
119.000000 inf nan nan nan
121.000000 inf nan nan nan
123.000000 inf nan nan nan
125.000000 inf nan nan nan
127.000000 inf nan nan nan
129.000000 inf nan nan nan
131.000000 inf nan nan nan
133.000000 inf nan nan nan
135.000000 inf nan nan nan
.......
.......
Is that I'm doing umbrella sampling in wrong way? That is shuold I take
the no. of windows more than 10 or 20? Dr. Grossfield told me that the
spring constant value in AMBER is in Kcal/radian**2 but his program reads
the spring constant as Kcal/degrees**2. Do I need to make these changes in
the spring constant value and submit it to the WHAM program? Please guide me
on this.
Thanks and regards,
Sai
On 2/2/06, Carlos Simmerling <carlos.ilion.bio.sunysb.edu> wrote:
>
> why is the # of windows equal to 1? that's not umbrella sampling.
>
> Sai Kumar Ramadugu wrote:
> > Dear Sir,
> > I tried using hormonic potential as u told in the earlier mail. I
> > used rk2=rk3=30.0. For the value of spring constant I doubled the
> > value and submitted to the WHAM. But the free energy is not calculated
> > properly. The output of HWAM is as follows:
> >
> > # ../../wham/wham 0.0 360.0 100 0.0 300.0 0 test1.out test1.o
> > #Number of windows = 1
> > # Dumping simulation biases, in the metadata file order
> > # Window F (free energy units)
> > # 0 nan
> >
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Received on Fri Feb 03 2006 - 06:10:10 PST
