My mdin file is:
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.
2015-11-25 23:02 GMT+08:00 David A Case <david.case.rutgers.edu>:
> On Wed, Nov 25, 2015, jinfeng liu wrote:
> >
> > 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.
>
> Something is wrong here. Can you post your mdin file? I fear that some
> unexpected combination of input parameters is leading to this result.
>
> ....dac
>
>
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Received on Wed Nov 25 2015 - 07:30:08 PST
