Hi Friends, I am working on peptide self assembly. I simulated two peptide which are random coil and apart from each other. As the time process they start to interact and form antiparallel beta sheet structure. My plan is to find the energy difference in random coil to beta shhet structure. I added protein1 protein2 group in mdp file I run g_energy coomand
Output: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. 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 Coul-SR:protein1-protein1 51 LJ-SR:protein1-protein1 52 LJ-LR:protein1-protein1 53 Coul-14:protein1-protein1 54 LJ-14:protein1-protein1 55 Coul-SR:protein1-protein2 56 LJ-SR:protein1-protein2 57 LJ-LR:protein1-protein2 58 Coul-14:protein1-protein2 59 LJ-14:protein1-protein2 60 Coul-SR:protein1-rest 61 LJ-SR:protein1-rest 62 LJ-LR:protein1-rest 63 Coul-14:protein1-rest 64 LJ-14:protein1-rest 65 Coul-SR:protein2-protein2 66 LJ-SR:protein2-protein2 67 LJ-LR:protein2-protein2 68 Coul-14:protein2-protein2 69 LJ-14:protein2-protein2 70 Coul-SR:protein2-rest 71 LJ-SR:protein2-rest 72 LJ-LR:protein2-rest 73 Coul-14:protein2-rest 74 LJ-14:protein2-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein .But when I gave the command : g_enemat_mpi -f ../energy.edr -groups groups.dat -etot ener.xvg I ended with following Missery : Opened ../energy.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):protein1-protein1 (0,0)in energy file WARNING! could not find group (null):protein1-protein2 (0,1)in energy file group 1WARNING! could not find group (null):protein2-protein2 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 200000 time 200000.000 Will build energy half-matrix of 2 groups, 6 elements, over 200001 frames Segmentation fault (core dumped) I will be thankful for any suggestion. Thank you in Advance. With best Wishes. -- 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