Dear Christoph, The dihedral was periodic from -180 to +180 C. I have shared the link for a dihedral. https://www.dropbox.com/s/5tzaf6krzj0cdsp/table_d2.xvg?dl=0
Chandan On Wed, Dec 3, 2014 at 1:39 AM, Christoph Junghans <[email protected]> wrote: > 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]. > 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/d/optout. > -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India *"All work and no play makes Jack a dull boy...”* -- 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/d/optout.
