Fixing bonds in dihydrogen phosphate to save computation time

From: Evgeny Bulat (
Date: Mon Jul 09 2012 - 13:55:45 CDT

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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