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.usc.es
Quoting Adrian Roitberg <roitberg.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.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.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.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
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Received on Sun Jan 13 2008 - 06:07:15 PST
