Following is the input file.
polymer
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 1, ntf = 1,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 1000000000, dt = 0.001,
ntpr = 1000, ntwx = 1000, ntwr = 1000
/
Hold atoms
500.0
ATOM 143
ATOM 389
END
END
atom 143 and 389 are the two ends of my two interacted polymer, the initial distance of the two atom is 11 angstrom. After 13ns simulation, the distance is 25 angstrom. I can see from the trajectoray file, the polymer moved freely, although slowly. I hope the two atoms don't move.
Thanks,
Xiaoquan.
2013-11-23
X Sun
发件人：case <case.biomaps.rutgers.edu>
发送时间：2013-11-24 05:28
主题：Re: [AMBER] Fix a atom??
收件人："AMBER Mailing List"<amber.ambermd.org>
抄送：
On Sat, Nov 23, 2013, X Sun wrote:
>
> I am trying to fix an atom of a polymer in my MD simulation to make a
> circumstance that the polymer is immoblized on some subtrate. At the
> beginning, I added a force constant 500kcal/mol to the atom, in tutorial
> B1, it said this was a very big number. But in my simulation, I found
> the atom moved around slowly. Should I increase the force constant? or
> is there any other method to fix one atom of a polymer in amber?
500 is indeed a big number. If you "fixed" atom actually moves (more than
a tiny amount, like 0.1 Ang) then there is probably something wrong with
how you are trying to restrain it. We'd need to know details of what you did
to be of any help.
>
> Additionally, is it possible to calculate free energy of some
> comformations in Amber?
Have you consulted Chap 4 ("Sampling and free energies") in the manual?
...dac
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Received on Sat Nov 23 2013 - 14:00:03 PST
