Why do I get this message saying the group is empty?
Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 11350 OTHER residues There are: 244 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... 0 System : 37770 atoms 1 Protein : 3848 atoms 2 Protein-H : 1980 atoms 3 C-alpha : 244 atoms 4 Backbone : 732 atoms 5 MainChain : 974 atoms 6 MainChain+Cb : 1206 atoms 7 MainChain+H : 1198 atoms 8 SideChain : 2650 atoms 9 SideChain-H : 1006 atoms 10 Prot-Masses : 3848 atoms 11 Non-Protein : 33922 atoms 12 LIG : 35 atoms 13 SOL : 33807 atoms 14 Na : 46 atoms 15 Cl : 34 atoms 16 Other : 33922 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom & 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit > 12 & 1 Copied index group 12 'LIG' Copied index group 1 'Protein' Merged two groups with AND: 35 3848 -> 0 Group is empty > 1 & 12 Copied index group 1 'Protein' Copied index group 12 'LIG' Merged two groups with AND: 3848 35 -> 0 Group is empty On Sat, May 22, 2010 at 9:57 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > John Shultz wrote: >> >> Justin, >> >> I finally got a chance to get back to this. I read the make_ndx >> instructions. Unless I am mistaken, I guess that is what you use to >> merge groups. >> > > Yep, that's the purpose of make_ndx. > > -Justin > >> Thanks, >> >> Jack >> >> On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> John Shultz wrote: >>>> >>>> Thank you Justin, is there a way I can choose both Protein LIG? It has >>>> the following options for me >>>> >>> You need to make a custom group that merges these two. >>> >>> -Justin >>> >>>> Reading toplogy and shit from md.tpr >>>> Reading file md.tpr, VERSION 4.0.5 (single precision) >>>> 50000 steps (100 ps) remaining from first run. >>>> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat >>>> Group 0 ( System) has 37770 elements >>>> Group 1 ( Protein) has 3848 elements >>>> Group 2 ( Protein-H) has 1980 elements >>>> Group 3 ( C-alpha) has 244 elements >>>> Group 4 ( Backbone) has 732 elements >>>> Group 5 ( MainChain) has 974 elements >>>> Group 6 (MainChain+Cb) has 1206 elements >>>> Group 7 ( MainChain+H) has 1198 elements >>>> Group 8 ( SideChain) has 2650 elements >>>> Group 9 ( SideChain-H) has 1006 elements >>>> Group 10 ( Prot-Masses) has 3848 elements >>>> Group 11 ( Non-Protein) has 33922 elements >>>> Group 12 ( LIG) has 35 elements >>>> Group 13 ( SOL) has 33807 elements >>>> Group 14 ( Na) has 46 elements >>>> Group 15 ( Cl) has 34 elements >>>> Group 16 ( Other) has 33922 elements >>>> Select a group: >>>> >>>> >>>> On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul <jalem...@vt.edu> >>>> wrote: >>>>> >>>>> John Shultz wrote: >>>>>> >>>>>> I am trying to rerun a simulation using this command >>>>>> mdrun -rerun -v -deffnm md >>>>>> >>>>>> I think I must have made a mistake when I prepared the original mdp >>>>>> file because I get this message >>>>>> Number of atoms in trajectory (3883) does not match the run input file >>>>>> (37770) >>>>>> >>>>>> I have these files in my directory >>>>>> Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp >>>>>> md_prev.cpt md.tpr md.trr md.xtc traj.trr >>>>>> >>>>>> Here is my mdp file, should I remove entries for xtc_grps and >>>>>> energygrps to avoid this issue? >>>>>> >>>>> You can, but it won't fix anything. Your original .xtc file saved only >>>>> the >>>>> coordinates of the Protein and LIG (per your output options), but your >>>>> .tpr >>>>> file has all of these atoms, regardless of what you choose to save. >>>>> You >>>>> can, however, create a .tpr file that has a just these atoms by passing >>>>> your >>>>> original .tpr file to tpbconv, using a suitable index group. >>>>> >>>>> -Justin >>>>> >>>>>> integrator = md >>>>>> nsteps = 50000 >>>>>> dt = 0.002 >>>>>> nstvout = 5000 >>>>>> nstlog = 500 >>>>>> nstenergy = 250 >>>>>> nstxtcout = 5000 >>>>>> nstxout = 5000 >>>>>> xtc_grps = Protein LIG >>>>>> energygrps = Protein SOL >>>>>> constraints = all-bonds >>>>>> nstcomm = 1 >>>>>> ns_type = grid >>>>>> rlist = 1.2 >>>>>> rcoulomb = 1.1 >>>>>> rvdw = 1.0 >>>>>> vdwtype = shift >>>>>> rvdw-switch = 0.9 >>>>>> coulombtype = PME-Switch >>>>>> Tcoupl = v-rescale >>>>>> tau_t = 0.1 0.1 >>>>>> tc-grps = protein non-protein >>>>>> ref_t = 300 300 >>>>>> Pcoupl = parrinello-rahman >>>>>> PcOupltype = isotropic >>>>>> tau_p = 0.5 >>>>>> compressibility = 4.5e-5 >>>>>> ref_p = 1.0 >>>>>> gen_vel = yes >>>>>> lincs-iter = 2 >>>>>> DispCorr = EnerPres >>>>>> optimize_fft = yes >>>>>> gen_seed = 805087 >>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> Justin A. Lemkul >>>>> Ph.D. Candidate >>>>> ICTAS Doctoral Scholar >>>>> MILES-IGERT Trainee >>>>> Department of Biochemistry >>>>> Virginia Tech >>>>> Blacksburg, VA >>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>>> >>>>> ======================================== >>>>> -- >>>>> gmx-users mailing list gmx-us...@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/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? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/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? Read http://www.gromacs.org/mailing_lists/users.php >>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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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