Re: Fixing bonds in dihydrogen phosphate to save computation time

From: Axel Kohlmeyer (
Date: Tue Jul 10 2012 - 05:21:14 CDT

On Tue, Jul 10, 2012 at 7:44 AM, Norman Geist
<> wrote:
> Hi,
> I think there’s no SHAKE like feature implemented for such usage. It’s also
> kind of a different simulation method, is mostly called “rigid body”.It is,
> as it seems, hard to combine with all atom force field, so there are no
> implementations I know in no classical md software.


this is an incorrect statement. codes like LAMMPS
or moldy do contain rigid body integrators.

the problem with a rigid body integrator, is that the
integration of the rotational degrees of freedom usually
still requires a fairly small time step to run stable.


> Possibly you could use the extrabonds command to introduce some strong
> forced angles/torsions/bonds to your ions to prevent them from moving to
> much within, this shouldn’t effect interaction with other molecules and
> could be worth a try.
> Regards
> Norman Geist.
> Von: [] Im Auftrag
> von Evgeny Bulat
> Gesendet: Montag, 9. Juli 2012 20:56
> An:
> Betreff: namd-l: Fixing bonds in dihydrogen phosphate to save computation
> time
> Hey everyone,
> Recently, I have explored using dihydrogen phosphate, H2PO4-, for ionizing
> my biomolecular MD simulation. The reason is that H2PO4- is more
> physiological than, say, Cl-. After generating H2PO4- toppars and ionizing
> the system, I performed 10ns of equilibration and noticed that, not
> surprisingly, the computation time is significantly slower than when Cl- is
> used; in fact, it's just not feasible at the moment.
> At this point, I'm looking into somehow freezing most bonds within H2PO4-,
> essentially modeling each anion as a rigid structure. I figure this may make
> the computation more permissible. I have looked into how NAMD can be used to
> freeze bonds between hydrogen and heavy atoms (with SHAKE), and wonder if a
> similar method has been developed (or can be developed) for specific bonds
> between heteroatoms.
> Thanks a bunch for any feedback.
> Best,
> Jack Bulat,
> Dept. of Bioengineering, UC Berkeley

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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