Thanks for your detailed answer Bill.
On Tue, Oct 31, 2017 at 2:16 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> You should read up on equilibration, e.g. see discussion of ntt=3 here:
>
> http://ambermd.org/tutorials/basic/tutorial1/section3.htm
>
> Bill
>
>
> On 10/30/17 9:32 PM, David Sáez wrote:
> > Hi, I am working on a very short QM/MM simulation and having some
> problems
> > to understand the temperature control. This is the input file I am using:
> >
> > QM/MM Molecular Dynamics
> > &cntrl
> > nstlim=10000, dt=0.0005, imin=0, ntpr=2000, ntwx=2000, ntwr=2000,
> > tempi=300.0,temp0=300.0, ntt=1, tautp=2.0, ig=209858, irest=0, ntx=1,
> > ntc=1, ntf=1, cut=8.0, ntb=1,
> > ifqnt=1
> > /
> > &qmmm
> > qmmask='.13722-13777',
> > qmcharge=0,
> > qm_theory='dftb3',
> > qmshake=1,
> > qm_ewald=1, qm_pme=1
> > /
> >
> > Coordinates are read from an energy minimization rst file, so I assigned
> > tempi=300.0 and temp0=300.0. Since the dynamics is very short, I was
> > expecting to have a constant temperature from the beginning.
> >
> > It started at 299.40 K, but later temperatures were:
> >
> > 1 ps: 188.22K
> > 2 ps: 212.79K
> > 3 ps: 231.05K
> >
> > and so on. Is this normal and I should give the simulation more time to
> > reach the 300K value, or am I doing something wrong?
> >
> > Thanks!
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>
>
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Received on Tue Oct 31 2017 - 15:00:02 PDT
