---------- Forwarded message ---------- From: rama david <[email protected]> Date: Wed, Dec 26, 2012 at 9:55 PM Subject: About g_enemat problem To: [email protected]
Hi Gromacs friend. I simulated a system containing random peptide I found that as they start to interact they change there secondary conformation. I want to determine the interaction potential energy of two peptide only. I make new mdp file containing the energygrps protein1 and protein2 I rerun the mdrun Now When I gave the command g_enemat it replied like Opened md-rerun.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 100000 time 100000.000 Will build energy half-matrix of 2 groups, 6 elements, over 100001 frames Segmentation fault (core dumped) I face the same problem in another system also... but when I wrote the command g_energy I received 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-SOL 61 LJ-SR:protein1-SOL 62 LJ-LR:protein1-SOL 63 Coul-14:protein1-SOL 64 LJ-14:protein1-SOL 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-SOL 71 LJ-SR:protein2-SOL 72 LJ-LR:protein2-SOL 73 Coul-14:protein2-SOL 74 LJ-14:protein2-SOL 75 Coul-SR:SOL-SOL 76 LJ-SR:SOL-SOL 77 LJ-LR:SOL-SOL 78 Coul-14:SOL-SOL 79 LJ-14:SOL-SOL 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein Where am I wrong ??? Is there any other way to do these ??? I also want to check the change in entropy of sol and protein ..How to check it ??? Please give me the suggestion.I will be a very thankfull to you. With Best Wishes and regards, Rama david -- 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
