Re: temperature calculations from velocities in NAMD?

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sun Nov 08 2009 - 19:24:12 CST

Dear Axel,
>> 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?
>>
>
>
> 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.

Thank you, so I can calculate n_DOF for the water molecules now because
I know that two bonds and one angle are constrained for each water molecule.

However, for (non-water) heavy atom hydrogens, I cannot tell whether the
NAMD command "rigidBonds all" only constrains bonds, or also (which)
angles, etc., as is done for the waters.

I took a look at the NAMD source code, but "grep"ing the whole source
code folder for
"rigidBonds"
"RIGID_ALL"
"SHAKE"
did not yield anything about additional angle, dihedral,... constraints.

Also, the most current paper (2009) on CHARMM refers to SHAKE only in
terms of "fixing the relative positions of..."

Can I thus assume that "rigidBonds all" really only constrains bonds
(for hydrogens attached to non-water heavy atoms)? If no, what angles
does NAMD "rigidBonds all" constrain for the protein?

Thank you very much for your help,
Best,
Sebastian

>> 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
> simulation
> 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).
>
> cheers,
> axel.
>
> 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
>>>
>>
>
>
>
>

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