[gmx-developers] The development of a new implementation of Rahman Parrinello
mrshirts at gmail.com
Tue Oct 11 03:32:12 CEST 2005
Sorry I haven't responded sooner, I've been on the road.
> I have heard that a new implementation of the Rahman Parrinello code
> is under development. All I know is that it uses a verlet velocity
Yes, I've been working with a lot of this locally. I have velocity
verlet implemented, along with Andersen version of pressure control -
which takes care of the isotropic case. It has been extended to
non-isotropic cases --see the references in the the Moldy manual,
which has a good basic outline at
http://www.earth.ox.ac.uk/~keithr/moldy-manual/node14.html. I have to
fiddle around with the different implementations of anisotropic
pressure control to figure out which one is going to work the best.
If you have any suggestions. I have not yet committed changes to the
main CVS yet.
> Is this implementation based in any reference in the bibliography?
Again, check out the references listed here:
> Would also include a reversible move for the Nose Hoover thermostat?
This is definitely in the plan, but I haven't quite got around to this
yet. If you have any particular implementations you think are
particularly good, let me know. Because of some committments here,
it may take a little longer to get these changes in, but I estimate
that they will almost certainly be in by the end of the year.
Going over this a little more, I think the best idea is to essentially
have two tracks -- one that leads to the current default path
(Berensen temperature and temperature control), and a separate track
that has velocity verlet, shake + rattle, exact pressure control
(which requires velocity verlet to be rigorously correct, and so forth
-- I don't think it's going to be necessary to mix and match all the
options, necessarily. Please let me know if anyone has any other
thoughts on this -- I'm soliciting ideas to make sure I don't miss
> Message: 2
> Date: Fri, 07 Oct 2005 08:34:24 +0200
> From: Berk Hess <hessb at mpip-mainz.mpg.de>
> Subject: Re: [gmx-developers] The development of a new implementation
> of Rahman Parrinello.
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <434616F0.30704 at mpip-mainz.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> ramon at juguete.quim.ucm.es wrote:
> >I have heard that a new implementation of the Rahman Parrinello code
> >is under development. All I know is that it uses a verlet velocity
> >Is this implementation based in any reference in the bibliography?
> This will come, the exact algorithm has not been decided yet.
> >Would also include a reversible move for the Nose Hoover thermostat?
> Gromacs 3.3 contains a reversible Nose Hoover leap-frog integrator.
> gmx-developers mailing list
> gmx-developers at gromacs.org
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