Hi Chandan, was your tabulated dihedral potentials actually periodic?
Cheers, Christoph 2014-01-06 9:47 GMT-07:00 Christoph Junghans <[email protected]>: > Sorry for the late replay, but I don't really have a good answer to > your question. > > Maybe you could try to: > - run the cg simulation without dihedrals and see how much the > distributions actually differ. If it isn't a lot you might don't even > need diheral interactions. > - do the IBI of the dihedrals at the very end, when the non-bonded, > angle and bond are already fitted. dihedrals are usually weak > interactions, so that should work. > - if your bonds can stretch a lot you might need to help gromacs to > guess their max lengths, so that you don't run into a domain > decomposition error (use -rdd option of mdrun) > > Cheers, > > Christoph > > 2013/12/9 Chandan Choudhury <[email protected]>: >> 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. > > > > -- > Christoph Junghans > Web: http://www.compphys.de -- Christoph Junghans Web: http://www.compphys.de -- 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]. 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