On Tue, Nov 17, 2015 at 8:14 AM, zhonghe xu <zhonghexu01.163.com> wrote:
> Hi Amber Users:
>
>
> I performed constant pH simulation with explicit water model using Amber14.
> During relaxation phase(turned off constant pH module), the temperature
> of system could
> be maintained well. In production phase(turn on pH module), however, the
> temperature of system（in
> output）were generally 50 K lower than targeted temperature (300K). The
> control parameter for constant pH
> simulation are listed below:
> &cntrl
> imin=0, irest=0, ntx=1, ntpr=10000, ntr=10000, ntwx=10000,
> nstlim=2000000,
> ig=-1, dt=0.002, ntt=3, tempi=300, temp0=300, gamma_ln=2.0,
> ntc=2, ntf=2, cut=10, iwrap=1, ntb=1, ntp=0,
> ntxo=2, ioutfm=1, icnstph=2, ntcnstph=200,
> solvph=4.0, ntrelax=200, saltcon=0.1,
> ntr=1, restraint_wt=10.0,
> restraintmask='.1',
> /
> Is there any wrong in my input. Thanks in advance!
>
T
his has been reported before (see
http://archive.ambermd.org/201507/0331.html
). It's a reporting issue caused by the fact that the temperature is
calculated and reported *before* the velocities for the frozen solute are
properly restored. The temperature is *actually* close to the target 300 K
(as per usual simulations), but the reported value is too low (since it
uses velocities of 0 for the solute when in reality they are much higher).
I'm trying to remember if I fixed this problem or not, but the issue will
hopefully be fixed before the next release.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 17 2015 - 05:30:05 PST
