Re: temperature calculations from velocities in NAMD?

From: Axel Kohlmeyer (
Date: Sun Nov 08 2009 - 11:17:20 CST

On Sat, Nov 7, 2009 at 9:13 PM, Sebastian Stolzenberg
<> wrote:
> ... Apologies, just saw the NAMD note on SHAKE *angles* for water.

on top of that, you can "shake" water molecules just as easily by defining
and constraining an H-H bond on top of the two O-H bonds. this is what many
MD codes are doing (and this is why you see an H-H bond in the waters, if you
load an AMBER generated toppar file or a CHARMM generated .psf)

> I assume now that the SHAKE algorithm imposes restraints on all the IC
> coordinates involving the particular hydrogen to be constrained.

that is not correct. you constrain what you define to constrain. typically,
the water molecules completely and all other bonds involving hydrogens.

> Then, what if I have a hydrogen attached to a backbone nitrogen? What about
> hydrogens attached to carbons along the side chains?

> I am worried to have to deal with dihedral constraints to determine
> n_DOF..... although the original SHAKE paper by RYCKAERT JCP 1977 does not
> mention dihedrals...

i don't think an over 30 year old paper is a good reference for modern
techniques. the same goes for the NAMD tutorial. the former is just the original
idea (nobody reads the original ewald sum paper to learn how to implement ewald
sum in a modern MD code), the latter is a means to get you started _without_
presenting too many confusing details.

why don't you have a look at some of the (many) more recent books
on MD simulation techniques and papers about the implementation of
current package MD codes (there is at least one for every major MD package
and i would recommend to not discard those about packages you don't use).


p.s.: since you are curious about methods, you should take note that SHAKE
is only half the story and that you have your constrained bonds
RATTLEd as well. ;)

> Thanks a bunch,
> Sebastian
> Sebastian Stolzenberg wrote:
>> Hi Axel,
>>> very simple: each "shaken" bond or angle is equivalent to removing one
>>> DOF. so waters have 6 DOFs instead of 9. if you go to more complex
>>> constraints it can become very complicated.
>> SHAKE *angles*?? The NAMD tutorial doesn't mention anything about them.
>> Or was your reasoning now more in general for educational purposes?
>> Would you have some DOF reading recommendations at hand for the more
>> complicated (e.g. dihedral) constraints cases? (just for my own curiosity
>> and to maintain my astonishment :o) )
>> Thanks a lot,
>> Sebastian

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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