[Bulk] 回复:Re: [Bulk] [gmx-users] a question about potential energy
Yang Ye
leafyoung at yahoo.com
Sun Aug 12 18:19:26 CEST 2007
hi,
my suggestion is still the previous one, get g_energy to plot a Energy
vs. time for you so you will know where this average value comes from.
Regards,
Yang Ye
On 8/12/2007 10:34 AM, taojinwuhan at sohu.com wrote:
>
> Dear Yany Ye
>
> Thank you for your help. I am indeed a new man as you guess. I am very
> very sorry about what I did and will take care to never make such stupid
> mistakes.
>
> The simulation I posted is a eq run, and I extracted the
> protein potential energy following what you taught me before(just want
> to check
> the protein). What puzzled me is that the potential energy in every
> frame is almost
> lower than -90000(you can see it in protein.xvg in attachment),but the
> average protein
> potential energy in log is just -188 and the RMS-fluctuations is
> 4146(see below).
> How did gromacs get the avergae value and rms value like these?
> According to my
> understanding the average energy should also be about -90000. Does my
> md run bad?
> Could you give me a explanation or give me any suggestions? Thanks!
>
> Best regards
>
> Paul Tao
>
>
> Ps: the part of log
>
> <====== ############### ==>
> <==== A V E R A G E S ====>
> <== ############### ======>
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 4.47120e+01 2.05332e+01 1.46051e+01 8.86024e+00 2.87573e+02
> LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential
> -9.50660e+01 -3.65730e+00 -1.01766e+02 -3.63918e+02 -1.88123e+02
> Kinetic En. Total Energy Temperature Pressure (bar)
> 6.82162e+01 -1.19907e+02 6.09296e-01 -1.52389e-01
>
> Box-X Box-Y Box-Z Volume Density (SI)
> 3.03565e-02 3.03565e-02 3.03565e-02 6.82831e+00 1.49606e-01
> pV
> -3.09662e+01
>
> Total Virial (kJ/mol)
> 3.78382e+01 7.27218e-01 -1.68112e-01
> 7.27214e-01 3.77270e+01 -8.52153e-01
> -1.68124e-01 -8.52145e-01 3.91003e+01
>
> Pressure (bar)
> -1.49730e-01 -9.56125e-03 3.10000e-03
> -9.56121e-03 -1.44637e-01 5.64105e-03
> 3.10011e-03 5.64098e-03 -1.62801e-01
>
> Total Dipole (Debye)
> -2.13479e+01 -2.18829e+01 -2.22107e+01
>
> <====== ############################### ==>
> <==== R M S - F L U C T U A T I O N S ====>
> <== ############################### ======>
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 9.89738e+02 4.53448e+02 3.23204e+02 1.94891e+02 6.34017e+03
> LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential
> 2.09723e+03 8.06436e+01 2.24368e+03 8.02594e+03 4.14647e+03
> Kinetic En. Total Energy Temperature Pressure (bar)
> 1.50381e+03 2.64284e+03 1.34318e+01 3.54340e+00
>
> Box-X Box-Y Box-Z Volume Density (SI)
> 6.69374e-01 6.69374e-01 6.69374e-01 1.50584e+02 3.29814e+00
> pV
> 7.19966e+02
>
> Total Virial (kJ/mol)
> 8.49070e+02 8.20897e+01 7.54720e+01
> 8.20897e+01 8.50494e+02 9.04527e+01
> 7.54718e+01 9.04529e+01 8.81896e+02
>
> Pressure (bar)
> 3.57605e+00 8.22075e-01 7.49848e-01
> 8.22075e-01 3.55242e+00 8.78451e-01
> 7.49846e-01 8.78454e-01 3.95141e+00
>
> Total Dipole (Debye)
> 4.70706e+02 4.82556e+02 4.89913e+02
>
> ----- 原文 -----
>
> *From:* Yang Ye <mailto:leafyoung at yahoo.com>
> *To:* Discussion list for GROMACS users
> <mailto:gmx-users at gromacs.org>
> *Subject:* Re: [Bulk] [gmx-users] a question about potential energy
> *Sent:* Sat Aug 11 11:41:35 CST 2007
>
>
>
>
> Hi,
>
> You shall help yourself to find the answer by plotting your energy
> with
> g_energy.
>
> Have your equilibrated your system well? Which stage of simulation are
> you running with, em, eq or production run? Having large
> fluctuation is
> sometimes normal and sometimes bad.
>
> Also, please attach necessary and concise information to the mails. We
> may open a table-like file (e.g. xvg) for energy but not a log
> file just
> for energies. I understand that you could be new to gromacs, just take
> note of this.
>
> Regards,
> Yang Ye
>
> On 8/10/2007 3:54 PM, taojinwuhan at sohu.com
> <mailto:taojinwuhan at sohu.com> wrote:
> >
> > Hi, all
> >
> > I have found a problem that in my Md run the potential energy in
> every
> > frame was about -9e+04 while the average potential energy of all was
> > -1.88e+02. What is wrong with it? Why are they so different? Can
> > anybody tell me the reason? Thanks!
> >
> > pS: the attachement is the md.log. You can clearly see that the
> > average energy is so different with the energy in each frame in it.
> >
> > Paul
> >
> >
> >
> >
> ------------------------------------------------------------------------
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