Amber Users,
I am trying to use time averaged restraints to refine a DNA solution
structure. On page 109 of the amber 9 manual, it says the default value for
the exponential decay constant is 1.0D+6. What does the "D" mean? I want a
decay constant on the order of pico seconds. My input file is as follows
where DISAVE value1 is 20e-12 for my time constant:
-#tg production run . 300K: 100ps MD, NMR RST; time avg
- &cntrl
- imin = 0, irest = 1, ntx = 7,
- ntb = 2, pres0 = 1.0, ntp = 1,
- taup = 2.0,
- cut = 15,
- nmropt = 1,
- pencut =-0.001,
- ntpr = 200,
- ntc = 2, ntf = 2,
- tempi = 300.0, temp0 = 300.0,
- ntt = 3, gamma_ln = 1.0,
- nstlim = 50000, dt = 0.002,
- ntpr = 100, ntwx = 100, ntwr = 1000
- /
- &wt type='DISAVE',value1=20e-12,value2=3, /
- &wt type='DISAVI',istep2=10,value1=0, /
- &wt type='END' /
-DISANG=17RST
-LISTOUT=POUT
Here I am trying to use 20 fs for value1, in my output file, I get the
follow bit of text:
- Begin reading energy term weight changes/NMR restraints
- WEIGHT CHANGES:
- DISAVE 0 0 0.000000 3.000000 0 0
- DISAVI 0 10 0.000000 0.000000 0 0
-
- RESTRAINTS:
- Requested file redirections:
- DISANG = 17RST
- LISTOUT = POUT
My concern is that it has 0.000000 for my time constant. I can not tell if
this is because it does not print enough significant figures in the output
file or if my input value is not recognized.
Any comments would be most welcome.
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Received on Sun Apr 01 2007 - 06:07:15 PDT
