Thanks Justin!
On Sat, May 22, 2010 at 10:12 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > John Shultz wrote: >> >> 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 >> > > The use of & tells make_ndx to write out a group that is the intersection of > these two. If there are no overlaps, the group is empty. What you want is > the "or" operator: > > 12 | 1 > > -Justin > >> >> >> >> 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 >>> >> > > -- > ======================================== > > 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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