On Thu, Feb 27, 2014, James Luginsland wrote:
>
> I am a new user & need a little help. I am working with a large system.
> This system has a protein called CDC 20 and approximately 1100 waters. When
> I run my simulations, I set the temperature to room temperature (298K)
> however, when the simulation runs, the temperature increases and levels out
> between 305-310K. How can I fix the temperature to stay at 298K & does this
> have anything to do with a "taup"? This simulation is being worked on AMBER
> 10.
The taup variable deals with pressure, not temperature. Look at the "ntt"
varible to control temperature. Using ntt=3 and gamma_ln=5.0 should work well
for most systems.
Aside: 1100 waters is a very small number for a protein the size of CDC20 (ca.
500 residues). It sounds like you might be in "no-man's land" between
implicit and explict water models. You don't have to reply, but make sure
that your system setup makes sense. Generally, as a new user, you should
either remove all the waters (and use a GB model for solvent), or add lots
of additional waters via a LEaP command like solvateBox.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 27 2014 - 19:30:02 PST
