Hi, I got the result by g_energy. Thank you for these . but when I used g_enemat with the edr file ( out put from mdrun -rerun ) g_enemat -f ener.edr -groups groups.dat i got following out put
roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 50000 time 10000.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) i used the following groups.dat file 2 extra34 energy What is reason for the error ?? Is I did any mistake again?? Thank you in advance. With best wishes and regards, Rama david On Fri, Oct 5, 2012 at 10:32 PM, rama david <ramadavidgr...@gmail.com>wrote: > Hi justin, > Ok now I get > I have to modify mdp parameter .. > > Thank you, > With best wishes and regards, > Rama david > > On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 10/5/12 11:46 AM, rama david wrote: >> >>> Thank you for your Help. >>> >>> I did the following tc-groups >>> >>> tcoupl = V-rescale ; modified Berendsen thermostat >>> tc-grps = extra34 Non-Protein energy ; two coupling groups - >>> more accurate >>> tau_t = 0.1 0.1 0.1 ; time constant, in ps >>> ref_t = 310 310 310 ; reference temperature, one for each >>> group, in K >>> ; >>> >>> Energy contain the residues that i needed >>> extra34 contain all the remaining ligand and receptor atom >>> non-protein contain sol and ion. >>> >>> I got the energy file after mdrun -rerun >>> >>> I used the g_energy term >>> >>> It give me the following output >>> End your selection with an empty line or a zero. >>> ------------------------------**------------------------------**------- >>> 1 G96Angle 2 Proper-Dih. 3 Improper-Dih. 4 >>> LJ-14 >>> 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 >>> Disper.-corr. >>> 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 >>> Kinetic-En. >>> 13 Total-Energy 14 Temperature 15 Pres.-DC 16 >>> Pressure >>> 17 Constr.-rmsd 18 Box-X 19 Box-Y 20 >>> Box-Z >>> 21 Volume 22 Density 23 pV 24 >>> Enthalpy >>> 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 >>> Vir-YX >>> 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 >>> Vir-ZY >>> 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 >>> Pres-XZ >>> 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 >>> Pres-ZX >>> 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 >>> Box-Vel-XX >>> 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X 48 >>> Mu-Y >>> 49 Mu-Z 50 T-extra34 51 T-non-Protein 52 >>> T-energy >>> 53 Lamb-extra34 54 >>> Lamb-non-Protein >>> 55 Lamb-energy >>> >>> >>> So I confused. though it shows the energy group, which option should i >>> have >>> to choose ?? >>> >>> What is Lamb-energy??? >>> >>> >> It is related to temperature coupling. >> >> >> Is I did any mistake??? or I have to use any else command ?? >>> >>> >> I have told you to use "energygrps" (which is described in the manual) >> and you're specifying "tc-grps." Temperature coupling and energy >> calculation groups are very different concepts. >> >> >> -Justin >> >> -- >> ==============================**========== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> ==============================**========== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
