You are jump-starting an unequilibrated block of ice to 300K. Short
answer is restrain your solute at first or warm gradually.
Bill
On 10/2/2015 1:58 PM, Kalenkiewicz, Andrew (NIH/NICHD) [F] wrote:
> 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
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Received on Fri Oct 02 2015 - 14:30:03 PDT
