[gmx-users] simulation using tabulated dihedral potentials.
Mark Abraham
mark.j.abraham at gmail.com
Mon Dec 9 13:12:02 CET 2013
Do your tabulated functions work on a toy system, like butane?
On Dec 9, 2013 6:47 PM, "Chandan Choudhury" <iitdckc at gmail.com> wrote:
> 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)
> I understand from the mailing list, that there are only handful of users
> actually using the tabulated potentials.
>
> Any insight will be very helpful.
>
>
> Chandan
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> --
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