[gmx-users] problem regarding "mdrun" and "g_hbond"

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 15 14:44:14 CET 2007

Hi Sangeeta, Mark,

Well, one, six, that's about the same thing (the same order of
magnitude at least). Maybe just over a handful, but all six of them
will be jostled around quite a bit by coupling to their private

I think a warning is a good idea, but maybe 10 is even on the low side
for that. Since temperature is macroscopic, you'll need enough atoms
not to deviate too much from the target temperature. I have no
evidence on which I can make a proper suggestion... My bidding will be
50! Going once, going twice... (maybe someone has looked more into
this matter. David, Berk?).


On 3/15/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > tc-grps             =  Protein  SOL   NA+
> > tau_t               =  0.1      0.1   0.1
> > ref_t               =  523      523   523
> This is a bad idea and we see it regularly on this mailing list. Coupling
> a single atom to a thermal bath is asking for trouble... what is the
> temperature of a single atom? Do you really want to be adding/taking
> random amounts of energy all the time?
> It's possible this explains your problem when you move to higher
> temperatures, but it makes everything else you've done suspect as well. A
> better approach is to couple to Protein and Non-Protein groups.
> Developers... how about a warning in grompp when a group has less than 10
> atoms or some such?
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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