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!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 30 2017 - 22:30:02 PDT
