AMBER Archive (2006)

Subject: Re: AMBER: Values of Spring Constants

From: Sai Kumar Ramadugu (compchem123_at_gmail.com)
Date: Wed Feb 01 2006 - 23:00:56 CST

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

The output file saved shows the following:

#Coor Free +/- Prob +/-
1.800000 nan nan nan nan
5.400000 nan nan nan nan
9.000000 nan nan nan nan
12.600000 nan nan nan nan
16.200000 nan nan nan nan
19.800000 nan nan nan nan
23.400000 nan nan nan nan
27.000000 nan nan nan nan
30.600000 nan nan nan nan
34.200000 nan nan nan nan
37.800000 nan nan nan nan
41.400000 nan nan nan nan
45.000000 nan nan nan nan
48.600000 nan nan nan nan
52.200000 nan nan nan nan
55.800000 nan nan nan nan
59.400000 nan nan nan nan
63.000000 nan nan nan nan
66.600000 nan nan nan nan
70.200000 nan nan nan nan
...............

Could u please suggest me anything on this?
Thanks and regards,
   Sai

On 2/1/06, David A. Case <case_at_scripps.edu> wrote:
>
> On Wed, Feb 01, 2006, Sai Kumar Ramadugu wrote:
>
> > Actually I was trying to understand the functioning of Umbrella
> Smapling.
> > For the same I took a protein of 40 aminoacids and did a GB simulation
> with
> > restraints on phi angle of 2nd amino acid which is Alanine.
> > My restraints input file is as follows:
> > # 2 ALA PHI: (1 ASP C)-(2 ALA N)-(2 ALA CA)-(2 ALA C) 120.0 180.0
> > &rst iat = 13, 15, 17, 23,
> > r1 = 119.0, r2 = 120.0, r3 = 180.0, r4 = 181.0,
> > rk2 = 2.0, rk3 = 2.0, &end
>
> To use WHAM, you need to define a harmonic potential, where r2=r3 and r1
> and
> r4 are far away from r2 and r3, as described on page 138 of the Users'
> Manual.
> The force constant will be twice the values you give for rk2=rk3 (because
> Amber historically does not include a factor of 1/2 in these constraint
> energies.)
>
> ...good luck...dac
>
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