AMBER Archive (2004)

Subject: AMBER: Re: AMBER: Temperature Regulation

Date: Wed Jul 28 2004 - 19:44:56 CDT

As well as checking the literature on how the simulations
are done, you would do well to figure out what water model
is appropriate. Almost all these models have some problems
with density, structure factor, hydrogen bonding distance,

Moreover, the standard water models in Amber are rigid.
When you go to very high pressures, quantum mechanics (QM) can
sure rear its ugly head. So _even if_ you were to successfully
calculate something out in that regime, it's hard to know if
you would obtain anything physically meaningful. You would
certainly need a non-rigid water model. The current model
you are using might fail even if you specify rigid water.
You should check RL Jernigan's work. My remote recollection is
that he didn't test these models at extreme pressures or
temperatures. You don't mention what model you are using.

Moreover, the parameters for any organic molecules would
also need to be optimized for that temperature and pressure
regime. You are probably looking at QM with sharp teeth,
powerful jaws and a fearsome roar.


>Dear All;
>We are running  periodic boundary condition dynamics on 432 ice system  
>in a rectangular box of size 19.074, 19.074, 38.148. we are interested  
>in a constant temperature and constant pressure simulation. In order  
>to get a higher  density of the ice to about 1.3 g/cm3, we set the  
>pressure to 10000 bars, the density came out as we expected but from  
>the output, we noticed that the temperature is far from the temperature  
>we want (temp0=50.0). Below are our input and output  files.

[remained snipped out]
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to