回复:Re: [Bulk] [gmx-users] a question about potential energy
taojinwuhan at sohu.com
taojinwuhan at sohu.com
Sun Aug 12 04:34:47 CEST 2007
<p> </p><p>Dear Yany Ye<br /><br />Thank you for your help. I am indeed a new man as you guess. I am very <br />very sorry about what I did and will take care to never make such stupid <br />mistakes.<br /><br />The simulation I posted is a eq run, and I extracted the<br />protein potential energy following what you taught me before(just want to check<br />the protein). What puzzled me is that the potential energy in every frame is almost <br />lower than -90000(you can see it in protein.xvg in attachment),but the average protein<br />potential energy in log is just -188 and the RMS-fluctuations is 4146(see below). <br />How did gromacs get the avergae value and rms value like these? According to my <br />understanding the average energy should also be about -90000. Does my md run bad?<br />Could you give me a explanation or give me any suggestions? Thanks!<br /><br />Best regards<br /><br />Paul Tao<br /></p><p><br />Ps: the part of log<br /></p><p><====== ############### ==><br /> <==== A V E R A G E S ====><br /> <== ############### ======><br /><br /> Energies (kJ/mol)<br /> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<br /> 4.47120e+01 2.05332e+01 1.46051e+01 8.86024e+00 2.87573e+02<br /> LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential<br /> -9.50660e+01 -3.65730e+00 -1.01766e+02 -3.63918e+02 -1.88123e+02<br /> Kinetic En. Total Energy Temperature Pressure (bar)<br /> 6.82162e+01 -1.19907e+02 6.09296e-01 -1.52389e-01<br /><br /> Box-X Box-Y Box-Z Volume Density (SI)<br /> 3.03565e-02 3.03565e-02 3.03565e-02 6.82831e+00 1.49606e-01<br /> pV<br /> -3.09662e+01<br /><br /> Total Virial (kJ/mol)<br /> 3.78382e+01 7.27218e-01 -1.68112e-01<br /> 7.27214e-01 3.77270e+01 -8.52153e-01<br /> -1.68124e-01 -8.52145e-01 3.91003e+01<br /><br /> Pressure (bar)<br /> -1.49730e-01 -9.56125e-03 3.10000e-03<br /> -9.56121e-03 -1.44637e-01 5.64105e-03<br /> 3.10011e-03 5.64098e-03 -1.62801e-01<br /><br /> Total Dipole (Debye)<br /> -2.13479e+01 -2.18829e+01 -2.22107e+01<br /><br /> <====== ############################### ==><br /> <==== R M S - F L U C T U A T I O N S ====><br /> <== ############################### ======><br /><br /> Energies (kJ/mol)<br /> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<br /> 9.89738e+02 4.53448e+02 3.23204e+02 1.94891e+02 6.34017e+03<br /> LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential<br /> 2.09723e+03 8.06436e+01 2.24368e+03 8.02594e+03 4.14647e+03<br /> Kinetic En. Total Energy Temperature Pressure (bar)<br /> 1.50381e+03 2.64284e+03 1.34318e+01 3.54340e+00<br /><br /> Box-X Box-Y Box-Z Volume Density (SI)<br /> 6.69374e-01 6.69374e-01 6.69374e-01 1.50584e+02 3.29814e+00<br /> pV<br /> 7.19966e+02<br /><br /> Total Virial (kJ/mol)<br /> 8.49070e+02 8.20897e+01 7.54720e+01<br /> 8.20897e+01 8.50494e+02 9.04527e+01<br /> 7.54718e+01 9.04529e+01 8.81896e+02<br /><br /> Pressure (bar)<br /> 3.57605e+00 8.22075e-01 7.49848e-01<br /> 8.22075e-01 3.55242e+00 8.78451e-01<br /> 7.49846e-01 8.78454e-01 3.95141e+00<br /><br /> Total Dipole (Debye)<br /> 4.70706e+02 4.82556e+02 4.89913e+02</p><blockquote style="border-left: 2px solid #000000; margin-left: 10px; margin-right: 0px; padding-left: 5px; padding-right: 0px; font-family: 宋体; font-style: normal; font-variant: normal; font-weight: normal; font-size: 9pt; line-height: normal; font-size-adjust: none; font-stretch: normal" dir="ltr"><div style="font-family: 宋体; font-style: normal; font-variant: normal; font-weight: normal; font-size: 9pt; line-height: normal; font-size-adjust: none; font-stretch: normal">----- 原文 ----- </div><br /><strong>From:</strong> <a href="mailto:leafyoung at yahoo.com">Yang Ye</a> <br /><strong>To:</strong> <a href="mailto:gmx-users at gromacs.org">Discussion list for GROMACS users</a> <br /><strong>Subject:</strong> Re: [Bulk] [gmx-users] a question about potential energy<br /><strong>Sent:</strong> Sat Aug 11 11:41:35 CST 2007<br /><p><br /><br /><br /> Hi,<br /> <br /> You shall help yourself to find the answer by plotting your energy with<br /> g_energy.<br /> <br /> Have your equilibrated your system well? Which stage of simulation are<br /> you running with, em, eq or production run? Having large fluctuation is<br /> sometimes normal and sometimes bad.<br /> <br /> Also, please attach necessary and concise information to the mails. We<br /> may open a table-like file (e.g. xvg) for energy but not a log file just<br /> for energies. I understand that you could be new to gromacs, just take<br /> note of this.<br /> <br /> Regards,<br /> Yang Ye<br /> <br /> On 8/10/2007 3:54 PM, <a href="mailto:taojinwuhan at sohu.com">taojinwuhan at sohu.com</a> wrote:<br /> ><br /> > Hi, all<br /> ><br /> > I have found a problem that in my Md run the potential energy in every<br /> > frame was about -9e+04 while the average potential energy of all was<br /> > -1.88e+02. What is wrong with it? Why are they so different? Can<br /> > anybody tell me the reason? Thanks!<br /> ><br /> > pS: the attachement is the md.log. You can clearly see that the<br /> > average energy is so different with the energy in each frame in it.<br /> ><br /> > Paul<br /> ><br /> ><br /> ><br /> > ------------------------------------------------------------------------<br /> > 《天龙八部》续作之“仙人指路”8月15日线上热播！<br /> > <<a href="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</a>><br /> ><br /> > *用搜狗拼音写邮件，体验更流畅的中文输入>><br /> > <<a href="http://goto.mail.sohu.com/goto.php3?code=mailadt-ta">http://goto.mail.sohu.com/goto.php3?code=mailadt-ta</a>><br /> ><br /> > ------------------------------------------------------------------------<br /> ><br /> > _______________________________________________<br /> > gmx-users mailing list <a href="mailto:gmx-users at gromacs.org">gmx-users at gromacs.org</a><br /> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br /> > Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br /> > Please don't post (un)subscribe requests to the list. 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