Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom.
On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/16/15 12:26 PM, gozde ergin wrote: > >> Thank for reply Justin but I have difficulty to understand which version >> has this bug? >> If 'Segmentation fault because of #DOF and frames numbers difference' is >> a >> bug than gromacs 4.6.3 is working correctly, right? >> >> > Offhand, I don't know which outdated versions work and which don't. To be > safe: > > 4.6.x series, use version >= 4.6.6 > 5.0.x series, use version 5.0.5 > Any other version in the development repo (master, release-5-0, etc) > > -Justin > > > >> >> >> >> On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 7/16/15 10:22 AM, gozde ergin wrote: >>> >>> Dear gromacs user, >>>> >>>> In order to estimate system absolute entropy value I want to use >>>> g_covar + >>>> g_anaeig commands. >>>> >>>> However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation >>>> fault after *'Diagonalizing ....'* step from gromacs 4.6.6 and 5.0.3. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> *Constructing covariance matrix (12258x12258) ...Last frame 4000 >>>> time >>>> 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 >>>> (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 >>>> (nm^2)Segmentation >>>> fault (core dumped)* >>>> >>>> But the same command, executed with g_covar of gromacs 4.6.3 works >>>> without >>>> any error or fault. >>>> >>>> Was it a bug and corrected for newer versions? I saw the release note >>>> of >>>> * >>>> 'Fixed a complicated bug in g_anaeig and g_covar, if the number of >>>> frames >>>> for a covariance analysis is fewer than the number of degrees of >>>> freedom' *for >>>> gromacs 4.6.6. >>>> >>>> >>>> The bug was also fixed for 5.0.5. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.