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

From: David A Case <>
Date: Thu, 26 Nov 2015 11:37:00 -0700

On Wed, Nov 25, 2015, jinfeng liu wrote:
> product MD
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=50000,dt=0.001,
> ntc=1,ntf=1,iwrap=1,
> ntp=1,taup=2.0,
> cut=12.0, ntb=2, igb=0,
> ntpr=1, ntwx=1, ntwr=1,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
> Actually, I was not performing the strict MD simulation. I performed a
> QM/MM-like MD simulation, where the water molecules in the QM zone could
> exchange with those in the MM zone, by using the combination of Amber and
> my own program.

A couple of extra notes, to add to my earlier email:

1. By using ntwx=ntwr=1 and cut=12.0, you will dramatically slow down the
simulation. Consider going to the default values if this is of importance to

2. It is certainly possible that the interaction of your program with Amber,
and/or the fact that this is QM/MM, could lead to problems with the Langevin
thermostat. This thermostat is quite sensitive to details, so it will be good
to try to track down the problem.


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Received on Thu Nov 26 2015 - 11:00:03 PST
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