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 as-is) 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:

-----Minimization-1

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

-----Minimization-2

guanine.3% less min1b.in
Energy minimization run 1a
 &cntrl
  imin=1, ncyc=250, maxcyc=1000, ntpr=5,
 &end

-----Equilibration-1

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

------Equilibration-2

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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