Hi justin,
g_enemat -f ener.edr -groups groups.dat -coul -nolj 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) Thank you in advance Rama david. > >> > Let me be a bit more specific again. I previously suggested there was a > problem with the -lj flag activating more than one option in the code, so > that is a potential problem. I suggested adding -nolj -coul to test this > theory. Please use those options (not -coul -lj) and see what happens. > > -Justin > > >> On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 10/8/12 5:40 AM, rama david wrote: >>> >>> Hi justin, >>>> >>>> As per your advice, >>>> >>>> g_enemat -f ener.edr -groups groups.dat -nocoul -nolj >>>> >>>> >>>> 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 0 elements >>>> Last energy frame read 50000 time 10000.000 >>>> Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames >>>> Segmentation fault (core dumped) >>>> >>>> What is the reason ??? >>>> >>>> >>>> I told you to add the -coul flag, not -nocoul. With the above command, >>> you're explicitly telling g_enemat to not do anything useful. >>> >>> >>> -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://vt.edu/Pages/Personal/justin> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================****========== >>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://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<h**ttp://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 [email protected]. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > 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 [email protected] > 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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
