AMBER Archive (2008)

Subject: AMBER: input options for replica exchange simulations

From: rebeca_at_mmb.pcb.ub.es
Date: Thu Jan 10 2008 - 10:46:42 CST

Hello,
I am trying to do replica exchange molecular dynamics using Amber9, but I don´t
have any experience in this type of simulations.
I would like to compare the results I will obtain with those simulations and
those obtained with the standar molecular dynamics, so I would like to use the
conditions of the calculations the most similar possible between them.

For the standar molecular dynamics I have used this input:

&cntrl
  imin=0, ntpr=1000, ntwx=1000, ntwe=1000, cut=12,
  irest=1, ntx=5, gamma_ln=0.2, ntwr=30000, nstlim=30000,
  ntb=2, ntf=2, ntc=2, ntp=1, ntt=3, temp0=300.0, dt=0.002,
 /

Could I use for the replica Exchange calculation an input like this one? It is
the same, but only adding numexchg = 2:

&cntrl
  imin=0, ntpr=1000, ntwx=1000, ntwe=1000, cut=12,
  irest=1, ntx=5, gamma_ln=0.2, ntwr=30000, nstlim=30000,
  ntb=2, ntf=2, ntc=2, ntp=1, ntt=3, temp0=300.0, dt=0.002, numexchg = 2,
&end
&ewald
&end

In the example of the test file, in Amber9, I could see they use another options
in the input, like constant volume and not using boundary conditions. Is there
any problem in doing such a calculation at constant pressure and using boundary
conditions? And what about ntt? In the example, ntt=1, and in my case ntt=3. Do
you know if there is any problem with that affects the results of the
simulation?

I hope anyone can help!

Best wishes,

Rebeca García Fandiño Ph.D.
Molecular Modeling & Bioinformatics
IRBB, Parc Cientific de Barcelona
C/Josep Samitier 1-5
08028 Barcelona
e-mail: regafan_at_usc.es

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