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, [EMAIL PROTECTED] 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:[EMAIL PROTECTED]> > *To:* Discussion list for GROMACS users > <mailto:gmx-users@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, [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> 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 > > > > > > > > > ------------------------------------------------------------------------ > > 《天龙八部》续作之“仙人指路”8月15日线上热播！ > > > > <http://ad1.adpolestar.net/ADPolestar/lgs/way/;er=&mv=710&pu=qiwei&ad=0018235?http://tl.sohu.com/?rcc_id=4bfd05b7d66287271b5738e9be7aae68 > > <http://ad1.adpolestar.net/ADPolestar/lgs/way/;er=&mv=710&pu=qiwei&ad=0018235?http://tl.sohu.com/?rcc_id=4bfd05b7d66287271b5738e9be7aae68>> > > > > *用搜狗拼音写邮件，体验更流畅的中文输入>> > > <http://goto.mail.sohu.com/goto.php3?code=mailadt-ta> > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search > before posting! > > Please don't post (un)subscribe requests to the list. 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Read http://www.gromacs.org/mailing_lists/users.php > > > > ------------------------------------------------------------------------ > 《天龙八部》续作之“仙人指路”8月15日线上热播！ > <http://ad1.adpolestar.net/ADPolestar/lgs/way/;er=&mv=710&pu=qiwei&ad=0018235?http://tl.sohu.com/?rcc_id=4bfd05b7d66287271b5738e9be7aae68> > > *用搜狗拼音写邮件，体验更流畅的中文输入>> > <http://goto.mail.sohu.com/goto.php3?code=mailadt-ta> > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? 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