AMBER Archive (2002)

Subject: About heating...

From: Andrei Leitão (ierdna_at_yahoo.com)
Date: Wed Dec 18 2002 - 12:23:43 CST

 Dear AMBER Users,

 I would like to know more about heating during the
molecular dynamic procedure.
 I am doing a molecular modeling study (500ps) to a DNA
decamer including explicit solvent molecules (H2O) and
counterions (Na+) at constant pressure.
 The input file is showed bellow:

  &cntrl

  ntx = 1, irest = 0, ntrx = 1, ntxo
  = 1,
  ntpr = 100, ntwx = 100, ntwv = 0, ntwe
  = 0,
  ntwprt = 0,

  ntf = 2, ntb = 2,
  cut = 12.0, nsnb = 10,

  ibelly = 0, ntr = 0,

  imin = 0,

  nstlim = 500000,
  t = 0.0, dt = 0.001,

  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  vlimit = 20.0,

  ntp = 1, pres0 = 1.0, comp = 44.6,
  taup = 0.2, npscal = 1,

  ntc = 2, tol = 0.00001,

 &end
 &ewald
 &end
 &wt
   type='TEMP0', istep1=0, istep2=10000,
                 value1=100.0, value2=300.0,
 &end
 &wt
   type='TEMP0', istep1=10000, istep2=500000,
                 value1=300.0, value2=300.0,
 &end

 I have problems to deal with some variables in the heating
protocol because the DNA molecule should be heated from
100K to 300K during the first 10ps. After that the system
would have to be in a constant temperature (300K) until the
end of the procedure.
 I made a molecular dynamic at 300K without this heating
procedure and one of the end base pairs was very distorted
from the axis.
 Is there any hint about that? I think that the high
temperature (300K) is related to it but I can not estimate
how much it is.
 That you very much about the hints.
 Merry Christmas.

=====
Andrei Leitão
Doutorando em Química Medicinal
Graduante Student in Medicinal Chemistry
NEQUIM - Núcleo de Estudos em Química Medicinal - Brasil
UFMG - Universidade Federal de Minas Gerais
NEQUIM - Medicinal Chemistry Group - Brazil
UFMG - Federal University of Minas Gerais

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