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:
# 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. 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! regards, Peyman > Choose appropriate energygrps in your .mdp file. > > -Justin > > Peyman Yamin wrote: > > Dear Gromacs users, > > > > I'm simulating dilute solutions of different surfactants in different > > media. All I want to analyse afterwards, though, is the single surfactant > > molecule properties! > > > > Is there any way to extract energy data from the original .edr file with > > respect to a single group, in the same way as one can extract structures > > from an .xdr with trjconvm? > > Is there any way to use g_energy to different groups? as I see I can only > > have some of the properties in a group-specified way - like T! I'm not > > asked in which group i'm interested and neither I can specify it at > > command-line, that I want, say total-energy of group G! > > > > Thanks in advance, > > > > Best regards > > Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] _______________________________________________ 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
