AW: Fixing bonds in dihydrogen phosphate to save computation time

From: Norman Geist (
Date: Tue Jul 10 2012 - 00:44:57 CDT



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.


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.




Norman Geist.


Von: [] Im Auftrag
von Evgeny Bulat
Gesendet: Montag, 9. Juli 2012 20:56
Betreff: namd-l: Fixing bonds in dihydrogen phosphate to save computation


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.

Jack Bulat,
Dept. of Bioengineering, UC Berkeley

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