you might need to use tighter temperature
coupling (reduce tautp) and see if that
helps with control. you may be getting fast
heating due to bad contacts and that energy
is hard to drain off without small tautp.
if that is the case, it may not be a good
sign because this rapid heating is probably
a sign of a problem somewhere in the structure.
using Berendsen scaling will give you the
temperature that you want but the distribution
of velocities may be undesirable.
carlos
----- Original Message -----
From: "Andrei Leitão" <ierdna.yahoo.com>
To: "AMBER list" <amber.heimdal.compchem.ucsf.edu>
Sent: Wednesday, July 09, 2003 4:25 PM
Subject: Temperature control
> 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,
>
> &end
> &ewald
> &end
> &wt
> type='TEMP0', istep1=0, istep2=10000,
> value1=100.0, value2=150.0,
> &end
> &wt
> type='TEMP0', istep1=10001, istep2=20000,
> value1=150.0, value2=200.0,
> &end
> &wt
> type='TEMP0', istep1=20001, istep2=30000,
> value1=200.0, value2=250.0,
> &end
> &wt
> type='TEMP0', istep1=30001, istep2=40000,
> value1=250.0, value2=300.0,
> &end
> &wt
> type='TEMP0', istep1=40001, istep2=500000,
> value1=300.0, value2=300.0,
> &end
>
> 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
