Re: Kb, Ktheta values for TIP3P water model

From: Axel Kohlmeyer (
Date: Tue Aug 05 2014 - 14:59:14 CDT

On Tue, Aug 5, 2014 at 3:49 PM, Hadi <> wrote:
> On Tue, Aug 5, 2014 at 12:29 PM, Kenno Vanommeslaeghe
> <> wrote:
>> Two questions:
>> (1) knowing that computers don't have infinite precision, there will
>> *always* be small deviations. The question to ask is: are they significant?
>> (2) Did you plot the same distribution for an MC simulation?
> Yes. My MC code does produce a distribution which is a delta function. As I
> mentioned, the NAMD results have slight deviations from a delta function.
> However, I quite agree with you: in addition to the previous factors
> (algorithm, rigid tolerance, time step), precision should be considered as
> well.

you have to be careful with generalizations in your statements. NAMD
is *one* MD code and the accuracy of SHAKE depends very much on the
length of the time step and convergence parameter. also, there are
*plenty other* MD codes that do offer to integrate rigid particles as
rigid bodies via separately integrating translation and rotation and
for those there is *not any* difference in the way how positions are
updated to what you do. as a person dealing with statistics and
distributions, you should know that a sample size of 1 doesn't allow
for much generalization, right?


Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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