Hi justin, I tried as per your suggestion.
command line g_enemat -f ener.edr -groups groups.dat -temp 310 -nolj -free the out put is like , Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 3 elements Last energy frame read 50000 time 10000.000 Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames Segmentation fault (core dumped) why program not work ?? Is it bug??? or Am I doing any stupid mistake??? Thank you in advance .. With best wishes and regards, Rama david On Sat, Oct 6, 2012 at 3:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/6/12 2:28 AM, rama david wrote: > >> Hi justin, >> >> the out put of g_energy are like >> >> ------------------------------**------------------------------**----- >> 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:energy-energy >> 51 LJ-SR:energy-energy 52 >> LJ-LR:energy-energy >> 53 Coul-14:energy-energy 54 >> LJ-14:energy-energy >> 55 Coul-SR:energy-extra34 56 >> LJ-SR:energy-extra34 >> 57 LJ-LR:energy-extra34 58 >> Coul-14:energy-extra34 >> 59 LJ-14:energy-extra34 60 >> Coul-SR:energy-rest >> 61 LJ-SR:energy-rest 62 >> LJ-LR:energy-rest >> 63 Coul-14:energy-rest 64 >> LJ-14:energy-rest >> 65 Coul-SR:extra34-extra34 66 >> LJ-SR:extra34-extra34 >> 67 LJ-LR:extra34-extra34 68 >> Coul-14:extra34-extra34 >> 69 LJ-14:extra34-extra34 70 >> Coul-SR:extra34-rest >> 71 LJ-SR:extra34-rest 72 >> LJ-LR:extra34-rest >> 73 Coul-14:extra34-rest 74 >> LJ-14:extra34-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 >> >> >> >> >> When I used g_enemat with the groups.dat file like these >> >> 2 >> extra34 >> energy >> >> I got the output >> >> >> 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) >> >> >> Now When I changed the groups.dat like >> >> 2 >> energy >> extra34 >> >> ( change in the order of the index groups ) >> >> I got the following output, >> >> Opened ener.edr as single precision energy file >> Will read groupnames from inputfile >> Read 2 groups >> group 0WARNING! could not find group (null):energy-energy (0,0)in energy >> file >> WARNING! could not find group (null):energy-extra34 (0,1)in energy file >> group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy >> file >> >> Will select half-matrix of energies with 6 elements >> Last energy frame read 50000 time 10000.000 >> Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames >> Segmentation fault (core dumped) >> >> >> > Based on the energy names, this is the appropriate setup, but > unfortunately I have no idea why it does not work. I have noticed that > there is a problem with g_enemat - the -lj flag specifies both LJ-SR and > LJ-LR terms to be written - which may be complicating matters. Please try > your command with -nolj to test. > > > >> >> So What is wrong ?? >> Is I am doing any wrong ?? >> >> >> >> 2. I am using the temp 310 so the reference temp by default is 300 >> Should >> I have to change it to 310 >> >> (-temp real 300 reference temperature for free energy >> calculation ) >> >> > As stated in the description, the -temp option is for free energy > calculations. Are you requesting a free energy calculation? You haven't > provided your command line. > > > -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? 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