AMBER Archive (2003)

Subject: Re: AMBER: constant energy simulation

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Tue Aug 12 2003 - 17:25:37 CDT

Actually I try to design a dipole which has vibration frequency around
10cm-1. After running MD I am going to use quaish program to analyze the
frequency to see whether I can get the same number (in principle I
should). Then I am going to do MD for this molecule in water to see
whether there is a frequency shift due to the solvent collision with the
dipole(We think there might be). The reason why I do this is because
last time I use quasih program to do analysis for a organic molecule, I
got several very low frequencies which should not be right.

Lishan

On Tue, 2003-08-12 at 15:51, Xavier Periole wrote:
> When you compare your total energy and your potential (very small)
> and kinetics energies, it is clear that your system is "flying" : too much
> kinetics energy. Which you can also see through your temperature :
> 763 K that is a lot, no !!
>
> Your are simulating a diatomic in vaccum !! No solvent = no friction !!
> your potential energy is all tranfered into kinetic energy.
>
> The problem is why are simulating a diatomic in vaccum in a MD programm.
> For this sytem you can do it ab initio !!
>
>
> Hope it helps
> XAvier
>
>
>
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-- 
Lishan Yao <yaolisha_at_pilot.msu.edu>
MSU

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