And please replicate it with a more recent 4.5.x or 4.6.x first! Mark
On Sun, Jul 7, 2013 at 3:17 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/6/13 8:21 AM, rama david wrote: >> >> 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) >> >> > > This problem has been posted several times before and looks buggy to me. > Please open a redmine issue and provide a sample input file that reproduces > the problem. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Associate > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > > -- > 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 -- 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
