Hi,
Try to restart each run adding TEMP0=300, IREST=1,
Greeting,
Hector.
> Dear Amber users,
>
> I am trying to start an accelerated MD simulation from an equilibrated
> system using a random seed (ig=-1) for the velocities, but for some reason
> there is a large temperature spike at the beginning of my simulation when
> I use the following input file:
>
> molecular dynamics run
> &cntrl
> imin=0, irest=0, ntx=1,
> ntt=3, tempi=300.0, gamma_ln=2.0,
> ig=-1, ntp=0, ntb=1, ntc=2, ntf=2,
> cut=10.0, nsnb=20, dt=0.002,
> nstlim=2500000, ioutfm=1,
> ntwe=200, ntwx=200, ntpr=50,
> iamd=3,
> EthreshD = 14744.2984, alphaD = 606.2,
> EthreshP = -365669.03, alphaP = 25317.8,
> &end
>
> The temperature starts at ~430K, drops to around 270K, and then
> equilibrates to 300K. But according to the manual:
>
> "For the initial dynamics run, (NTX .lt. 3) the velocities are assigned
> from a
> Maxwellian distribution at TEMPI K."
>
> Therefore why isn't the initial temperature at my specified value of 300K?
>
> Thanks,
> Andrew
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------
Dr. Héctor A. Baldoni
Departamento de Química
Área de Química General e Inorgánica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 02 2015 - 21:30:03 PDT
