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 -- 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]. 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