AMBER Archive (2005)

Subject: AMBER: Equilibration MD

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Sat Sep 03 2005 - 00:55:22 CDT

Dear AMBER users,

I am trying to run an equilibration md of a system
solvated in TIP3P waterbox. I wish to decrease the
restraints on the molecule in steps. In the first
cycle the system is heated up to 300K in 10ps. In the
next cycle I want to reduce the restraint force. But
when I do this the initial temperature is much
large(447.92K). My input files are attached. Please
look into this and suggest what is wrong.

Thanking you,
Mathew
i/p for the first step
-------------------------------------------------------
ade bulge: 10ps MD with res on DNA
 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 50000, dt = 0.002,
  ntpr = 500, ntwx = 500, ntwr = 1000,
  nmropt = 1,
 /
 &wt type = 'TEMP0', istep1 = 0, istep2 = 50000,
value1 = 0.0, value2 = 300.0,
 /
 &wt type = 'END'
 /
Keep DNA fixed with weak restraints
10.0
RES 1 17
END
END
-------------------------------------------------------

input I tried for the second step
-------------------------------------------------------
ade bulge: 10ps MD with res on DNA 5kcal
 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 50000, dt = 0.002,
  ntpr = 500, ntwx = 500, ntwr = 1000,
/
Keep DNA fixed with weak restraints
5.0
RES 1 17
END
END
--------------------------------------------------------

/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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