[gmx-users] pressure / compressibility
spoel at xray.bmc.uu.se
Wed Sep 17 14:41:01 CEST 2003
On Wed, 2003-09-17 at 13:26, m b wrote:
> der GMX-users,
> I am somewhat confused about one issue in
> NPT simulations and I'd very much appreciate
> if anybody could enlighten me.
> I understand that when doing a constant
> pressure simulation one has to give not only
> the pressure but also the compressiblity
> as input parameter (at least in some cases,
> in which ??)
> I would have thought that the compressiblity
> is a material property and hence ought to be
> calculated from the output of a simulation
> rather than given in the input ?
> (doesn't giving both compr. and P as input
> overdetermine the ensemble in some way ?)
> In some parts of the docu it is suggested to
> use 4.5e-05 as the compressibility when simulating
> aqueous systems.
> What if I simulate other materials, e.g., a
> crystalline system ?
> For many substances accurate experimental
> values for the whole compressibility matrix
> are not known.
the compressibility modulates the pressure coupling. Equations are in
the manual. The reason for inputting a compressibility is that you can
have a coupling constant in comprehensible units (i.e. ps), if you
select a compressibility that is close enough to the real value, that
You can indeed compute compressibility from the simulation too, most
often one uses some fluctuation formula. Check one of the simulation
text books (e.g. Allen and Tildesly). An other route would be to do a
series of simulations at different pressure and compute dV/dP
> Even if I know these values I still cannot be
> sure if my simulation would be consistent
> because I would expect the actual compressibility
> of the system to depend VERY sensitively on
> the forcefield used, and then the input
> and the compressibility corresponding to the
> simulated system, geometry and forcefield might
> differ considerably, possibly resulting in
> all sorts of artefacts ??
> grateful for any comments!
> Michael Brunsteiner
> RDMCh, Agfa-Gevaert
> Do you Yahoo!?
> Yahoo! SiteBuilder - Free, easy-to-use web site design software
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users