Dear all,
I am facing some weird problem while using tabulated potentials (esp. dihedral tabulated potentials) in gromacs 4.6.3. I am trying to generate a coarse grained (CG) trajectory using the tabulated potentials generated for the atomistic simulations using VOTCA. When I donot use the dihedral tabulated potentials, the simulations seems to proceed smoothly. The problem arises when the dihedral potentials are incorporated. I have added a link of all the files generated during the undermentioned runs (https://www.dropbox.com/s/yumzdufuys1ifdr/with-dih.tar) . It also includes the input files. Here, I list the problem and how do they occur : 1. $mdrun_463 -v -nice 0 -cpt 1 -cpi state.cpt -nt 2 -pin on (1st Run) >& ver1.txt Progress smoothly for few steps (step 536400). Shows the following error : A list of missing interactions: Tab. Dih. of 720 missing 1 Molecule type 'POLCAR' the first 10 missing interactions, except for exclusions: Tab. Dih. atoms 6 7 8 9 global 858 859 860 861 ------------------------------------------------------- Program mdrun_463, VERSION 4.6.3 Source code file: /tmp/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393 Fatal error: 1 of the 2400 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Sometimes Life is Obscene" (Black Crowes 2. Then I continue the run using the state.cpt file $mdrun_463 -v -nice 0 -cpt 1 -cpi state.cpt -nt 2 -pin on >& ver2.txt Further progressed for few more steps (step 973100). Following error is produced here: A list of missing interactions: Tab. Angles of 800 missing 1 Tab. Dih. of 720 missing 1 Molecule type 'POLCAR' the first 10 missing interactions, except for exclusions: Tab. Dih. atoms 9 10 11 12 global 237 238 239 240 Tab. Angles atoms 10 11 12 global 238 239 240 Back Off! I just backed up dd_dump_err_0_n1.pdb to ./#dd_dump_err_0_n1.pdb.1# Back Off! I just backed up dd_dump_err_0_n0.pdb to ./#dd_dump_err_0_n0.pdb.1# ------------------------------------------------------- Program mdrun_463, VERSION 4.6.3 Source code file: /tmp/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393 Fatal error: 2 of the 2400 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "She's a Good Sheila Bruce" (Monty Python) 3. Again continued the simulation $mdrun_463 -v -nice 0 -cpt 1 -cpi state.cpt -nt 2 -pin on >& ver3.txt Simulation proceeds for further for step 3692700. The again crashed with the following output: A list of missing interactions: Tab. Angles of 800 missing 1 Tab. Dih. of 720 missing 2 Molecule type 'POLCAR' the first 10 missing interactions, except for exclusions: Tab. Dih. atoms 6 7 8 9 global 306 307 308 309 Tab. Angles atoms 7 8 9 global 307 308 309 Tab. Dih. atoms 7 8 9 10 global 307 308 309 310 Back Off! I just backed up dd_dump_err_0_n0.pdb to ./#dd_dump_err_0_n0.pdb.2# Back Off! I just backed up dd_dump_err_0_n1.pdb to ./#dd_dump_err_0_n1.pdb.2# ------------------------------------------------------- Program mdrun_463, VERSION 4.6.3 Source code file: /tmp/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393 Fatal error: 3 of the 2400 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Though the path of the comet is sure, it's constitution is not" (Peter Hammill) In this way the simulations proceed. At the end it finally stops at step 71768380 and no further continuation is possible. Error at this stage : Started mdrun on node 0 Mon Dec 9 12:24:52 2013 Step Time Lambda 71768380 358841.90000 0.00000 Energies (kJ/mol) Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR) 5.18063e+03 6.57460e+03 8.27504e+02 1.20890e+04 0.00000e+00 Potential Kinetic En. Total Energy Temperature Pressure (bar) 2.46717e+04 1.12236e+04 3.58953e+04 9.38392e+02 4.95772e+03 DD step 71768389 load imb.: force 0.5% Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Tab. Dih. of 720 missing 1 Molecule type 'POLCAR' the first 10 missing interactions, except for exclusions: Tab. Dih. atoms 9 10 11 12 global 45 46 47 48 ------------------------------------------------------- Program mdrun_463, VERSION 4.6.3 Source code file: /tmp/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393 Fatal error: 1 of the 2400 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I donot understand why the simulations shows these errors and again it continues further for few more steps. In the topology file all the interactions are mentioned. A point is to be noted here that when I comment the dihedral sections in the topology the simulation proceeds very smoothly. All the files are uploaded here (https://www.dropbox.com/s/yumzdufuys1ifdr/with-dih.tar) Any insight will be very helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Chandan kumar Choudhury NCL, Pune INDIA -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
