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 - 14:00:03 PDT
