Frankie Montenegro wrote:
Wow, I didn't realize you guys in Europe work 24/7 too. On Sunday morning
nonetheless :-)
new on the list? (I know you're not...)
On 10/14/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
question: are there chemical bonds between "molecules" (which you seem
to imply by stating the sites are connected by an aromatic ring). If
there are then your whole system should be considered as a single
molecule. Have you tried x2top on this? (gmx 3.3.2 only).
Yes they are. x2top wouldn't work, most atoms are redefined (two types
of O with
different charges, two types of C, etc. All are custom-fitted with
Gaussians and GULP) I don't think treating the whole system as one
molecule could work. A single "cell" of the crystall would have over
250 atoms, and I need 2x2 structure minimum, probably even bigger. But
that might be last resort (after all , aren't some proteins over
couple of thousand atoms?)
you can tune x2top as you see fit by editing the ffoplsaa.n2t file. Size
is not a problem, and you can use periodic molecules as well.
Not sure what you're after, but I hope you realize that GROMACS can only
do pair potentials, so no funky non-bonded three body potentials.
BTW, what is the slope of GMX_performance vs. molecule_size curve ?
There is one more regrouping that I am trying right now (namely having two
moleculetypes: "cube-edge" and "cube-node", adding some table "LJ" in between).
If this doesn't go, I am out of ideas. Thanks anyway.
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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