AMBER Archive (2005)

Subject: Re: AMBER: GB with Langevin dynamics problem 2

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Fri Apr 08 2005 - 12:55:48 CDT

Hi,
> The result shows constant and large translational movement of the
> molecule.
...What is large and what is constant? With Langevin-dynamics, COM
translation gets what it deserves according to the equipartition theorem
(on the average). I guess if it is a small ("light-weight") molecule, it would
travel around quite a bit due to diffusion.
COM rotation behaves like COM translation. So, periodically removing COM
translation and rotation one would expect downwards jumps in KE Trans and
KE Rot. In my opinion, one should not remove COM motion when using Langevin
dynamics. For keeping the molecule "in place", one could now and then
just re-set the COM to the origin (that's somewhat like following the
molecule's overall motion with a camera).
Alternatively, one could remove COM motion every timestep. It depends
on the way Langevin dynamics is implemented whether that's easily possible
in a physically sound way.

> Lastly, has anyone carried out long and reasonable
> Langevin simulation with Amber 8?
> ... not with amber8, but with NAB (5.0 is just out!). Three 15ns
simulations for testing purposes ran without any problem. I just didn't
remove COM motion. To be sure I just took the power spectrum of E_Kin
(from part of one run).
Result: More or less white noise with a moderate low-frequency peak as
expected. Amber8 and nab5 should give identical results (besides different
random seeds) I hope.

Of course I can't guarantee there are no bugs, but I don't think so.

I hope that helps,
Andreas 

-- 

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                        svrci_at_tbi.univie.ac.at
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