Subject: Re: CCL:md, equilibriation times and vibrations

From: [email-masked] (Dr. Eric P. Wallis)
Date: Thu, 22 Sep 1994 14:23:20 +0100

I encountered this same problem working on a gas-phase molecule of 21 atoms. 
 I was using velocity scaling, i.e., isokinetic techniques to mimic a 
canonical system.  I noticed that my potential and internal kinetic energy 
were very much smaller that 3/2kT.  Since I was in the gas phase, the 
translational and molecular rotational motions were virtual infinite sinks 
for energy since there was no need (or way) for the molecule to transfer 
kinetic energy back out of these modes in the gas phase.  I fixed (worked 
around) the problem by initally subtracting our all of the translational and 
external rotational motion.  Than, everytime I scaled the velocities to 
adjust the temperature, I would again subtract out the external motions.  
Since I was not interested in translational and external rotational motion 
of the molecule, this solved the problem.  I don't know if this would work 
for your system or not.  Hope this helps.
Eric
>I've encountered a problem with MD that experienced modellers may be able to 
>put my mind to rest about.  Taking an isolated molecule (a mere 28 atoms) 
>which had been loosely geometry optimized, I turned it loose in a molecular 
>dynamics simulation using PM3 and monitored a few bond torsions and the 
>potential energy. (1 fs time step and .1ps bath relaxation).  The potential 
>energy slowly drifted downward and after 20ps seemed to be assymptotically 
>approaching a binding energy of -2542 kcal/mole.  During this time the 
>torsions which I was observing noticeably damped down substantially. 
> Afterwards I optimized the molecule, getting an energy of about -2546 
>kcal/mole and started a new md run with the new structure with a heating 
>period of 1 ps to 300C.  The potential energy leaped up about 25 kcal/mole 
>which seems about right (28 * 3/2 *(RT=.6kcal/mole)).  The potential energy 
>is slowly settling back down and presumably will approach -2542 kcal/mole 
>again.  Observing the damping out of the torsions and the small change in the 
>mean potential energy (4kcal/mole) between the minimized structure and the 
>equilibrium one, has lead to worry about where are the zero point vibrations. 
> When the simulations are started the atoms are given randomn directions 
>which basically excites all sorts of modes.  As the molecule deexcites and 
>the bath carts off the excess energy all the bond vibrations (bends, 
>stretches and torsions) seem to be disappearing so that one is left with a 
>molecule travelling through space and spinning but that's all.  I dusted off 
>my trusty old QM textbook and looked up 1-d harmonic oscillators.  It pointed 
>out that zero point energy (that 1/2h(nu)) is a quantum mechanical effect 
>arising from the non-commutation of the positon and momentum operators (i.e. 
>the Heisenberg uncertainty principle raises its ugly head).  Now in a 
>computer simulation of a molecule there is no such problem about commutation. 
> I can know both the position and momentum of the nuclei to arbitrary 
>accuracy.  Does this mean that if I wait long enough the vibrations will all 
>freeze out completely and I'll be left with a spinning molecule careening 
>through space.  One might also point out that it will be spinning and 
>careening far too fast since the bath will make sure the overall kinetic 
>energy, alot of which should be tied up in vibrations, is correct.  Obviously 
>in a liquid, inter-molecular interactions will cause randomization of some 
>sort and pump energy back into vibrational modes.  However, the whole thing 
>leaves me a little concerned about these kind of calculations.  Can someone 
>out there reassure me?
>
>Ross Underhill
>[email-masked]
>
>
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* Eric P. Wallis, Ph.D                                        *
* Computational Chemistry                                     *
* Phillips Petroleum Company       Office  (918)-661-7956     *
* 331A PL PRC                      FAX:    (918) 662-1097     *
* Bartlesville, OK 74004           email:   [email-masked]      *
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