AMBER Archive (2008)

Subject: Re: AMBER: input options for replica exchange simulations

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jan 10 2008 - 10:57:12 CST

you cannot use constant pressure for REMD in Amber. Check the work by Garcia
on
constant P REMD, there are many issues to consider. The most obvious is that

at the high temperatures in REMD, the water will vaporize at 1atm.
Additionally, one
needs to consider pressure in the exchange calculation.
different ntt values should be fine, as long as you use a thermostat.

On Jan 10, 2008 11:46 AM, <rebeca_at_mmb.pcb.ub.es> wrote:

> 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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