AW: [gmx-users] Re: Conceptual question: Why are MD production simulations usually run in the NVT ensemble?
dommert at icp.uni-stuttgart.de
Sun Jul 15 13:44:00 CEST 2012
> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] Im Auftrag von Andrew DeYoung
> Gesendet: Samstag, 14. Juli 2012 18:56
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] Re: Conceptual question: Why are MD production
> simulations usually run in the NVT ensemble?
> Hi Justin,
> Thanks so much for your time.
> You make a very good point about NPT. My field (although I am only a
> year graduate student) is physical chemistry, and I am ignorant,
> of biochemical literature.
> In physical chemistry, it seems that people almost always use NVT for
> production simulations, but I am not sure why, because just as in
> experiments, I would expect NPT to be more realistic -- chemicals (whether
> a pure liquid, like in "my" field, or a solvated biomolecule, like in
"your" field) are
> usually exposed to atmospheric pressure in experiments. In experiments,
> volume is usually not fixed, I think. So it makes sense you say that
> simulations are typically performed in NPT. I don't know why physical
> experiments on, and simulations of, liquids would be any different.
I completely understand your question, because it also came up to me. As
Justin mentioned, NpT simulations are the common situation for biophysical
processes in cells, because it is their native environment. The minimum of
the Gibb's free energy G=H+pV determines the system state. Assuming you are
performing an equilibrium MD, G is a constant of motion. Now the task of the
integrator including the thermostat and barostat is to keep G constant. If
you perform an NVT simulation you have no control over G but only the
Helmholtz free energy H=U-TS. Hence if you are interested in a certain state
of the system like folding of a protein or free energies, which depend on G
you have to simulate the corresponding ensemble. If you want to study
thermodynamic properties such as density, conductivity, diffusion, the
choice of the ensemble depends on other reasons. If you want to study the
density, an NVT simulation is not useful, because you set the density as
input parameter. However, if you are able to extract the desired data from
an NVT ensemble, it is preferable to an NpT simulation, because you do not
have to assure that the barostat couples correctly and the sampling is
sufficient to have no bias from the barostat. This is especially important
if you are studying new compounds, where the system is not well study such
that a proper adjustment of the barostat parameters is difficult. Sometimes
it is also difficult to sample canonically in an NpT ensemble, if the
simulation time is short, the system is small or the virial theorems are not
sufficiently fulfilled for other reasons. The common protocol to equilibrate
in NpT and perform a production run in NVT is finally related to Justin's
comment regarding the parameterization. An equilibration of the system can
only be achieved, if the system is allowed to get into the corresponding
state given by the force field. If you would have a "perfect" force field,
you could also skip the NpT equilibration, because with the knowledge of the
experimental density you could setup your system in the correct state and
sample in an NVT ensemble. At the end in the NVT production run you only
have to assure that you sample long enough to obtain a reliable average of
dynamic properties, like diffusion or conductivity, such that they are not
biased by the thermostat.
This is my opinion to this matter and I hope it helps, but please correct
my, if I am wrong.
> I guess then this could be an issue of the field? Are there chemists or
> reading this that can please provide advice?
> Best wishes,
> Andrew DeYoung
> Carnegie Mellon University
> gmx-users mailing list gmx-users at gromacs.org
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users