AMBER Archive (2008)

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

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Jan 10 2008 - 11:28:50 CST

Also, keeping nstlim at 30000 means that an exchange will be attempted
ONLY after 30000 steps, so you would not gain anything
against the same time for MD.

I think you should use nstlim ~ 500 or 1000 (amber 10 should allow you
to use much lower nstlim without getting hit on performance)

One more thing, if you are able to recompile amber yourself, I recommend
you add
-DNO_DETAILED_TIMINGS to the AMBERFLAGS in config.h). This helps with
less writing and accelerates REMD potentialy quite a bit.

Adrian

Carlos Simmerling wrote:
> 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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> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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