Temperature control

From: Andrei Leitão <ierdna.yahoo.com>
Date: Wed, 9 Jul 2003 17:25:12 -0300 (ART)

 Dear AMBER users,

 I am performing a molecular dynamic step on a set of short
DNA olygomers (heptamers) and it appeared a question about
the heating procedure.
 First, I made a heating procedure without any kind of
refined control but now I am trying to do the same job
again with a temperature control, i.e., my system should be
heated 200K (from 100K to 300K) during 40ps. It is an
average heating of 5K per 1ps.
 Unfortunately, my procedure failed completely, the system
heated 200K in only 15ps (this is the same result that I
got before without any specific temperature control).

The last step (MD):
  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  vlimit = 20.0,

   type='TEMP0', istep1=0, istep2=10000,
                 value1=100.0, value2=150.0,
   type='TEMP0', istep1=10001, istep2=20000,
                 value1=150.0, value2=200.0,
   type='TEMP0', istep1=20001, istep2=30000,
                 value1=200.0, value2=250.0,
   type='TEMP0', istep1=30001, istep2=40000,
                 value1=250.0, value2=300.0,
   type='TEMP0', istep1=40001, istep2=500000,
                 value1=300.0, value2=300.0,

 Should I use any kind of specific flag or change some
values of them to run this procedure?
 Best regards,

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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Received on Wed Jul 09 2003 - 21:53:01 PDT
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