[AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics

From: jinfeng liu <jinfengliu1119.gmail.com>
Date: Wed, 25 Nov 2015 16:23:40 +0800

Dear Amber users,

Recently, I performed molecular dynamics of the liquid water in TIP3P
model. After the system was heated to 300K and equilibrated in 300 ps, I
run the producution simulation. The temperature was controlled using the
Langevin dynamics (ntt=3, gamma_ln=2.0) durig the production simulation.
However, the equilibrium temperature (305K) was slightly higher than the
target temperature which was 300K. So, I wonder, if it would make a
difference when I set the Gamma_ln to a larger value (5.0 for instance) ?
What should I do to effectively drive the temperature to the target ? And,
if I want to use the Andersen thermostat instead, what proper value of
vrand should set ? I see few people use the Andersen thermostat, are there
any disadvantages for this thermostat ?

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Received on Wed Nov 25 2015 - 00:30:03 PST
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