AMBER Archive (2007)

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

From: adelene_at_Stanford.EDU
Date: Mon May 14 2007 - 15:17:28 CDT

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)
cut=25.0
nsnb=100
ntpr=1000
ntpr_md=1000
gamma_ln=50.0
tempi=50.0
gb=1
kappa=0.19

Is this due to the langevin dynamics options I have chosen? I've read
in the mailing list that some others have had problems with Langevin
Dynamics and MD before.

Thanks!

Adelene

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