Thanks for your reply. But sometimes I found that the liquid water dynamics
simulation without SHAKE would give more reasonable result, so I would
prefer to use SHAKE.
And, if it would make a difference when I set the Gamma_ln to a larger
value (5.0 for instance) ? 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 ?
2015-11-26 0:38 GMT+08:00 Daniel Roe <daniel.r.roe.gmail.com>:
> On Wed, Nov 25, 2015 at 8:24 AM, jinfeng liu <jinfengliu1119.gmail.com>
> wrote:
> > ntc=1,ntf=1,iwrap=1,
>
> TIP3P is a rigid water model and requires the use of SHAKE. So you
> need at least ntc=2 here.
>
> -Dan
>
> > 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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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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Received on Wed Nov 25 2015 - 18:00:10 PST
