I misspoke about unequilibrated, but even being equilibrated, the system
will have a sudden jump in temperature that reflects how the random
velocities interact with the force field.
Bill
On 10/2/2015 2:05 PM, Bill Ross wrote:
> 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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>
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Received on Fri Oct 02 2015 - 14:30:04 PDT
