**From:** Hadi (*dinpajooh_at_gmail.com*)

**Date:** Wed Aug 06 2014 - 13:57:26 CDT

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This thread started with a question about rigid models which use bond

constraints in MD simulations, i.e., when the structure can be defined by

bond constraints the network of bonds. This is one way to enforce a rigid

body in a simulation, i.e. by imposing a sufficient number of bond

constraints between the atoms in the unit. Therefore, in this thread I am

using the term "rigid model" to pertain to these methods.

Hadi

On Tue, Aug 5, 2014 at 12:59 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

*> On Tue, Aug 5, 2014 at 3:49 PM, Hadi <dinpajooh_at_gmail.com> wrote:
*

*> > On Tue, Aug 5, 2014 at 12:29 PM, Kenno Vanommeslaeghe
*

*> > <kvanomme_at_rx.umaryland.edu> wrote:
*

*> >>
*

*> >> Two questions:
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*> >>
*

*> >> (1) knowing that computers don't have infinite precision, there will
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*> >> *always* be small deviations. The question to ask is: are they
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*> significant?
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*> >>
*

*> >> (2) Did you plot the same distribution for an MC simulation?
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*> >
*

*> > Yes. My MC code does produce a distribution which is a delta function.
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*> As I
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*> > mentioned, the NAMD results have slight deviations from a delta function.
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*> > However, I quite agree with you: in addition to the previous factors
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*> > (algorithm, rigid tolerance, time step), precision should be considered
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*> as
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*> > well.
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*>
*

*> 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
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*> *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
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*> updated to what you do. as a person dealing with statistics and
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*> distributions, you should know that a sample size of 1 doesn't allow
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*> for much generalization, right?
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*>
*

*> axel.
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*>
*

*>
*

*>
*

*>
*

*>
*

*> --
*

*> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
*

*> College of Science & Technology, Temple University, Philadelphia PA, USA
*

*> International Centre for Theoretical Physics, Trieste. Italy.
*

*>
*

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