AMBER Archive (2004)Subject: AMBER: MD & folding
From: bybaker_at_itsa.ucsf.edu
Date: Tue Nov 02 2004  15:31:31 CST
('binary' encoding is not supported, stored asis)
Hello, Bimo:
Thank you very much for your advices.
It worthy to try running the MD at a longer time, such as 10 ns. This
might take about two months to finish. I am not sure I can do this. I
will give a try.
On the other hand, some literatures, such as Alonso et al 2001, showed
significant conformation changes on ptotein conformation during a 10 ns
MD run at pH 2.0. And the change was observed even at the first 2 ns
runs. In my cases, the two runs at different pHs are almost identical. I
am wondered if Amber force fields are suitable for such kind of unfolding
study.
By mistake I sent my input files as a Word attachment. Soory about that.
I have included the files at the end of this message.
All the bests.
Bo
Here is the input files:
Minimization1
guanine.2% less min1a.in
Minimization solvates with cartesian restriantes for the solute
&cntrl
imin=1, ncyc=250, maxcyc=1000, ntpr=5,
&end
Group input for restrained atoms
10.0
RES 1 214
END
END
Minimization2
guanine.3% less min1b.in
Energy minimization run 1a
&cntrl
imin=1, ncyc=250, maxcyc=1000, ntpr=5,
&end
Equilibration1
guanine.4% less 1md.in
Initial molecular dynamic run 1: heating up the system, equilibration stage 1:
&cntrl
imin=0, irest=0, ntx=1,
ntt=1, tempi=0.0, temp0=300.0, tautp=2, ig=209858,
ntp=0,
ntb=1, ntc=2, ntf=2,
nstlim=50000, dt=0.002,
ntwr=5000, ntwx=5000, ntpr=500,
&end
Equilibration2
guanine.5% less 2md.in
Initial molrcular dynamic run 2: constant pressure constant temperature
equilibration stage 2
&cntrl
nstlim=50000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
temp0=300.0, ntt=1, tautp=2.0,
ntb=2, ntp=1,
ntc=2, ntf=2,
nrespa=1,
&end
Production MD
guanine.6% less md1a.in
Initial molecular dynamic production run 1: constant pressure constant temp
&cntrl
nstlim=500000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
temp0=300.0, ntt=1, tautp=2.0,
ntb=2, ntp=1,
ntc=2, ntf=2,
nrespa=1,
&end
(END)

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