Re: [AMBER] confusions about some thermodynamic properties of TIP3P water

From: <>
Date: Mon, 18 Jul 2011 05:02:01 -0400 (EDT)


> I used TIP3P water model to simulate some properties for liquid water at
> 300k and 1atm.The result are based on averages covering 2ns.But the
> thermodynamic results, for example the isothermal compressibilities and
> isobaric heat capacity, are different from the calculated properties

Did you exactly replicate the simulations in your reference paper? Changes
in simulation length, cutoffs, electrostatics model, time-steps, etc. can
strongly influence your results. You do not give details about your
simulations and do not say how big the differences are that you see, so
its hard to judge if the results are reasonable.

Note that MD simulations (especially long ones) are not exactly
replicable. Due to round-off differences, trajectories diverge and you may
see slightly different results when running even the same simulation setup

> pointed by some paper using the same TIP3P water model .Please tell me
> what is the actual result or the range of the properties.

Im not sure there is an 'actual' result, the behaviour of a water model
will depend on the physical parameters used in the simulation.

Kind Regards,

Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Mon Jul 18 2011 - 02:30:03 PDT
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