Hi, On Sun, Jun 4, 2017 at 4:08 PM Apramita Chand <apramita.ch...@gmail.com> wrote:
> Dear All, > > When I'm trying to construct a RMSD matrix , using the command > g_rms -s protein_equili.gro -f protein_model1_ut.xtc -m > rmsd-matrix.xpm -tu ns > > I get the error: > Last frame 200000 time 20.000 > > Building RMSD matrix, 200001x200001 elements > element 28982; time 2.90 Killed > That matrix has 4x10^10 elements, each of which needs 4 bytes of memory. 1GB is about 1x10^9 bytes, so you'd need at least 160 GB of memory. The real issue is that you are probably using a large number of highly correlated frames, so even if you could form the full distance matrix, you would not learn any more than you would from a matrix formed from a suitable sub-sampling. > I have given the reference structure to be the one prior to production run > and after equilibration step. I have also tried the command with .tpr file. > Same error! > The problem doesn't change with the nature of the reference structure. Mark > How to solve this? > > > yours sincerely > Apramita > -- > 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.