Hi again, Now I remember! some old g_energy let me use numbers as the input for the terms I wanted...!
As you say, it looks like the total energy for different groups is not calculated. So I should somehow do it myself? If yes, I don't even know where I should get the terms I should add together from? I think I'd need all bonding and nonbonding interactions! or I should even calculate them? I can't also find what SR and LR and 14 mean in energy terms...! Would greatly appreciate any suggestion, Peyman On Monday 09 June 2008 18:27, Mark Abraham wrote: > Peyman Yamin wrote: > > On Monday 09 June 2008 16:19, Justin A. Lemkul wrote: > > > > Well, ofcourse I did! otherwise I wouldn't expect any program to know > > them by itself! the problem is that I say: > > Well, there's a lesson here. You should spell out all relevant data - > like your usage of energy groups in your run input file and your full > observations of g_energy the first time. We don't read minds here, and > Justin's assumption of your probable failure to plan for your own > analysis seems to be borne out by the way most new people approach MD > simulations :-) > > > # g_energy -f ../ener.edr -s ../25ns.tpr -b 23000 -e 25000 -skip 25 -o > > tot_ener > > > > and I get: > > > > > > Opened ../ener.edr as single precision energy file > > > > Select the terms you want from the following list > > ----------------------------------------------------- > > Angle Proper-Dih. Improper-Dih. LJ-14 > > Coulomb-14 LJ-(SR) Coulomb-(SR) Coulomb-(LR) > > RF-excl. Potential Kinetic-En. Total-Energy > > Temperature Pressure-(bar) Box-X Box-Y > > Box-Z Volume Density-(SI) pV > > Vir-XX Vir-XY Vir-XZ Vir-YX > > Vir-YY Vir-YZ Vir-ZX Vir-ZY > > Vir-ZZ Pres-XX-(bar) Pres-XY-(bar) Pres-XZ-(bar) > > Pres-YX-(bar) Pres-YY-(bar) Pres-YZ-(bar) Pres-ZX-(bar) > > Pres-ZY-(bar) Pres-ZZ-(bar) #Surf*SurfTen Pcoupl-Mu-XX > > Pcoupl-Mu-YY Pcoupl-Mu-ZZ Mu-X Mu-Y > > Mu-Z Coul-SR:OCT-OCT LJ-SR:OCT-OCT Coul-LR:OCT-OCT > > Coul-14:OCT-OCT LJ-14:OCT-OCT Coul-SR:OCT-TX1 LJ-SR:OCT-TX1 > > Coul-LR:OCT-TX1 Coul-14:OCT-TX1 LJ-14:OCT-TX1 Coul-SR:TX1-TX1 > > LJ-SR:TX1-TX1 Coul-LR:TX1-TX1 Coul-14:TX1-TX1 LJ-14:TX1-TX1 > > T-OCT T-TX1 Lamb-OCT Lamb-TX1 > > > > without any notification for choosing a group. > > Actually, that's all the notification you get. You can type a > newline-delimited list of the energy terms you'd like, and follow it > with a blank line and g_energy will produce your output. You may also > like to consult > http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive > > Note, however, that "total energy of group X" is not available. That's > because it isn't calculated, and in the vast majority of cases it > wouldn't mean anything anyway. You can see a breakdown of the nonbonded > interactions there, however. > > > On the other hand, for instance > > when I say: > > > > # g_gyrate -f out.xtc -s ../25ns.tpr > > > > I get, in a beautiful way: > > > > Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) > > Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) > > Opening library > > file /apps/GMX/331-intel64-intelmpi-wc/share/gromacs/top/aminoacids.dat > > Group 0 ( System) has 24476 elements > > Group 1 ( TX1) has 46 elements > > Group 2 ( OCT) has 24430 elements > > Select a group: > > > > Now I don't know why I don't get the same behaviour with g_energy, if at > > all I should expect such a thing! > > It's inconsistent, but probably reflects that a different person wrote > the two programs. > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > 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? Read http://www.gromacs.org/mailing_lists/users.php -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik University of Erlangen Egerlandstr. 3, 91058 Erlangen, Germany peyman.yamin AT cbi.uni-erlangen.de _______________________________________________ gmx-users mailing list [email protected] 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? Read http://www.gromacs.org/mailing_lists/users.php
