Thanks for your reply The following terms are present in my energy files
1 Angle 2 Proper-Dih. 3 Improper-Dih. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr. 8 Coulomb-(SR) 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 13 Temperature 14 Pres.-DC 15 Pressure 16 Constr.-rmsd 17 Box-X 18 Box-Y 19 Box-Z 20 Volume 21 Density 22 pV 23 Enthalpy 24 Vir-XX 25 Vir-XY 26 Vir-XZ 27 Vir-YX 28 Vir-YY 29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32 Vir-ZZ 33 Pres-XX 34 Pres-XY 35 Pres-XZ 36 Pres-YX 37 Pres-YY 38 Pres-YZ 39 Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42 #Surf*SurfTen 43 Box-Vel-XX 44 Box-Vel-YY 45 Box-Vel-ZZ 46 Mu-X 47 Mu-Y 48 Mu-Z 49 T-Protein 50 T-non-Protein 51 Lamb-Protein 52 Lamb-non-Protein So, please suggest why I am getting error, If the LJ-(SR) and Coulomb-(SR) terms are already present in the energy file. On Thu, Apr 14, 2011 at 00:36, Justin A. Lemkul <[email protected]> wrote: > > > bipin singh wrote: >> >> Hello, >> >> I am using g_enemat to calculate the energy matrix from the energy >> file(edr file) and I am supplying Protein as a group in -groups >> option. >> The command I am supplied is as follows: >> >> g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot >> energy.xvg -temp 328 -nocoul -nolj -nomean >> >> but I am getting the following error >> Read 1 groups >> group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy >> file >> >> As written in the manual: >> "Energy groups with names like ’Coul-SR:Protein-SOL’ and >> ’LJ:Protein-SOL’ are expected in the energy >> file" >> But I am not clear how to get these terms in energy file..... >> > > Whatever name you supply has to be an actual term in the .edr file. Run > g_energy first to get a list of all valid energy terms if you are unfamiliar > with the contents of the .edr file. > > -Justin > >> The energy file I am supplying is from a 100 ns md simulation. >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- ----------------------- Regards, Bipin Singh -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
