Hi, Your xtc file has only the group you wrote, so it isn't valid to index into it with an index file that was made for a conformation with many other atoms. That's the mismatch the message mentions. For your xtc, "System" is the subset of *it* that you seem to want for your analysis. Note that gmx convert-tpr -f topol.tpr -n -o subset.tpr is sometimes needed for giving an analysis tool a matching coordinate and trajectory file. That would let you then build eg a Protein group that was valid to index into your trajectory.
Mark On Fri, 28 Jul 2017 01:46 Jared Sagendorf <sagen...@usc.edu> wrote: > Hello, I'm using GROMACS 5.1.13 and ran into a problem I've never > encountered before. I've run a simulation on a zinc-finger DNA complex and > defined a group in my index filed called "Protein_DNA" from the default > "Protein" and "DNA" groups. This group should contain 4666 atoms, which it > does. > > $gmx make_ndx -n index.ndx > 0 System : 180141 atoms > 1 Protein : 2830 atoms <================== > 2 Protein-H : 1427 atoms > 3 C-alpha : 171 atoms > 4 Backbone : 513 atoms > 5 MainChain : 685 atoms > 6 MainChain+Cb : 851 atoms > 7 MainChain+H : 854 atoms > 8 SideChain : 1976 atoms > 9 SideChain-H : 742 atoms > 10 Prot-Masses : 2830 atoms > 11 non-Protein : 177311 atoms > 12 Ion : 32 atoms > 13 ZN : 7 atoms > 14 NA : 25 atoms > 15 DNA : 1836 atoms <================= > 16 ZN : 7 atoms > 17 NA : 25 atoms > 18 Water : 175443 atoms > 19 SOL : 175443 atoms > 20 non-Water : 4698 atoms > 21 Water_and_ions : 175475 atoms > 22 Protein_DNA : 4666 atoms <================= > > I'm not sure why the ZN and NA groups show up twice, but I assume it's not > an issue. Anyway, Protein_DNA is defined, and when I compare the values in > the index.ndx file to the atom numbers in the .gro file, it all matches up. > > In my .mdp input file, I specify this group to be output as a compressed > .xtc trajectory. > > ; OUTPUT CONTROL OPTIONS = > nstxout = 10000 > nstvout = 10000 > nstfout = 0 > nstlog = 10000 > nstenergy = 2500 > nstxout-compressed = 1000 > compressed-x-precision = 1000 > compressed-x-grps = Protein_DNA > > And then I run my simulation. I now have my traj.xtc file, which I want to > process. However, when using gmx trjconv, and select the group Protein_DNA, > I get the following error: > $gmx trjconv -f traj.xtc -n index.ndx [options] > Fatal error: > Index[4659] 4667 is larger than the number of atoms in the > trajectory file (4666). There is a mismatch in the contents > of your -f, -s and/or -n files. > > The group DNA_Protein should contain 4666 atoms, and I've verified that my > traj.xtc file indeed contains 4666 items with gmx check: > > $gmx check -f traj.xtc > Checking file traj.xtc > Reading frame 0 time 0.000 > # Atoms 4666 > ... > > So what is the problem here? The error message states that "Index[4659] > 4667 is larger than the number of atoms in the trajectory file (4666)", > which is true - the 4659th atom listed in the "Protein_DNA" index is indeed > atom 4667, but so what? There's 4666 atoms in the index, and 4666 atoms in > traj.xtc file - I don't see where the mismatch is. > > Can someone help me out with this and suggest some things to try, or > explain what is wrong if I'm missing something? > > Is it possible this is related to the fact that the protein topology file > includes 7 zinc atoms (since this is a ZF protein), which are not included > in the group Protein_DNA? Note that if I don't supply an index file and > choose "Protein" from the default groups, gmx > trjconv will run, but if I choose "DNA", I get a similar error. > > Fatal error: > Index[1829] 4667 is larger than the number of atoms in the > trajectory file (4666). There is a mismatch in the contents > of your -f, -s and/or -n files. > -- > 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.