AMBER Archive (2007)

Subject: Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB)

From: David A. Case (case_at_scripps.edu)
Date: Mon May 14 2007 - 16:40:50 CDT

On Mon, May 14, 2007, adelene_at_stanford.edu wrote:

> Hi, I've run some MD simulations (simulated annealing from 500 --> 400
> --> 300 with 100,000 steps per temperature), and realised that in my
> MD run, the energy and temperature fluctuations are rather large.
> (Total energy as
> given in the "MD:" row). Energy fluctuations are ~80kcal/mol, while
> temperature fluctuations are ~50K.
>
> Are these values to be expected? They seem far larger than what I
> would think MD should give.
>
> Here are my MD options:
> (1396 atoms, 1141 frozen)

If you really have only 45 moving atoms, you should expect very large
temperature fluctuations. This has been discussed earlier on the mailing
list:

 http://amber.ch.ic.ac.uk/archive/200608/0329.html

...hope this helps...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu