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 - 14:50:18 CST

that works fine, we've used standard PBC with REMD in these papers

**

Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A. and Simmerling,
C., *"Comparison of multiple Amber force fields and development of improved
protein backbone parameters"*, Proteins: Structure, Function and Genetics,
3:712-725 (2006).

**Wickstrom, L., Okur, A., Song, K., Hornak, V., Raleigh, D. and Simmerling,
C., *"The Unfolded State of the Villin Headpiece Helical Subdomain:
Computational Studies of the Role of Locally Stabilized Structure"*, J. Mol.
Biol., 360:1094-1107 (2006).

**Okur, A., Wickstrom, L., Layten, M., Geney, R., Song, K., Hornak, V. and
Simmerling, C., *"Improved Efficiency of Replica Exchange Simulations
through Use of a Hybrid Explicit/Implicit Solvation Model"*, J. Chem. Theory
Comput., 2:420, 2006.

Okur, A., Wickstrom, L. and Simmerling, C.,* "Evaluation of salt bridge
structure and energetics in peptides using explicit, implicit and hybrid
solvation models"*, J. Chem. Theory Comput., in press

On Jan 10, 2008 1:00 PM, <rebeca_at_mmb.pcb.ub.es> wrote:

> Thank you very much for your answers, they are very helpful. One more
> question:
> what about using periodic boundary conditions in the amber replica
> exchange
> simulations? In the manual I do not see clear if they can be used for
> explicit
> solvent REMD or only for using a hybrid solvent model.
> Thank you very much for your help,
>
> 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
>
>
>
> Quoting Adrian Roitberg <roitberg_at_qtp.ufl.edu>:
>
> > 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
> >>>
> >>>
> >>>
> -----------------------------------------------------------------------
> >>> The AMBER Mail Reflector
> >>> To post, send mail to amber_at_scripps.edu
> >>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >>>
> >>
> >
> > --
> > 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
> >
> ============================================================================
> >
> > To announce that there must be no criticism of the president,
> > or that we are to stand by the president right or wrong,
> > is not only unpatriotic and servile, but is morally treasonable
> > to the American public."
> > -- Theodore Roosevelt
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu