AMBER Archive (2007)

Subject: Re: AMBER: abnormal high temperature during NPT ensembles MD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Feb 27 2007 - 20:36:01 CST


perhaps it is the parameters?
was it stable for simulations at NVT?

On 2/27/07, ebright HMS <amber.hms_at_gmail.com> wrote:
>
> hi all :
>
> I am simulating a small organic molecule (coumarin-like ) in explicit
> water
> solvent by Amber 8. 1ns NVT ensemble equilibration run was first conducted
> to make
> sure the system equilibrate under constant volume. However, I observed
> very abnormal high temperature (above 400K) in the followed NPT ensemble
> production run although I set the temperature at 300K. It seems that the
> system
> is 'boiling' somehow. Can anybody give me some inputs why this happens ?
> Thanks ! I listed the production run input and output below. Additionally,
> I am
> not able to set the cut-off at 10 or 12 since it always complains " Ewald
> PARAMETER
> RANGE CHECKING: out of legal range".
>
>
> md3.in
> ------------------------
> NPT production MD
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 8, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 100000, dt = 0.002,
> ntpr = 100, ntwx = 500, ntwr = 1000
> /
> END
>
> md3.out
> -------------------------------------------------------------------------------------------------
>
> check COM velocity, temp: 0.017613 0.47(Removed)
>
> NSTEP = 13000 TIME(PS) = 1226.000 TEMP(K) = 626.92 PRESS =
> 7428.4
> Etot = -1117.9956 EKtot = 1337.9965 EPtot = -
> 2455.9921
> BOND = 3.8632 ANGLE = 8.2509 DIHED =
> 4.8641
> 1-4 NB = 6.6715 1-4 EEL = -32.0330 VDWAALS =
> 507.9005
> EELEC = -2955.5094 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 462.0735 VIRIAL = -1360.9398 VOLUME =
> 11366.1939
> Density =
> 0.9452
>
>
>
>
>
>
>
>
>
>

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