[gmx-users] flexible water vs. rigid water
albert_sun9 at yahoo.com
Fri Sep 12 16:58:00 CEST 2003
the unit 1fs = how many 1ps?
Why use smaller timestep - 1fs ?
Erik Lindahl <lindahl at stanford.edu> wrote:
On Thursday, September 11, 2003, at 08:28 PM, qiao rui wrote:
> Hi, Gromacs-er:
> I am curious whether the differnt water model can give different
> dynamic properties, especially viscosity? In particular, which is
> in terms of providing good viscosity - flexible water or rigid water?
> In addition, what is the major advanges of using flexible water
> rather than rigid water molecules? (rigid one is easier to implement,
> Is there a flexible SPC/E water model? If there is, how to include
> it in the Gromacs simulation?
Water is difficult, and I do not claim to be a world-leading authority
on the subject - let's see if other people fill in :-)
Some comments, though:
1. Normally, bond constraints are good since they are a much better
approximation of the quantum mechanical ground state than a classical
harmonic oscillator (flexible bond).
2. Water is a bit special, partly because we also keep the angle fixed,
but also because flexible bonds can help give the molecule
3. Models are usually parameterized for a specific case: either
flexible or fixed. While you might improve one of the properties by
using the other setup, the overall properties can often be worse.
4. It is almost impossible to minimize energy efficiently with fixed
5. You can just add defines = -DFLEX_SPC to get the flexible versions
of SPC or SPC/E, but it is mainly intented for energy minimization.
6. You might need to use a smaller timestep (1fs) with flexible waters.
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.
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users