Dear Justin and Mark, Thanks for the reply. I have regenerated the potentials for the bonded and non-bonded part. I observe the similar behavior as previous.
Keeping dihedral switched off, the simulation proceeds. Taking in account the dihedral, the simulation shows the similar behavior. Now, I switched off the two dihedrals (terminal ones). Out of 5 dihedral angles, two are switched off. The simulation proceeds smoothly for system consisting 10-chains (120 beads) for 200000000 steps. The problem is shown for the 80-chains (960 beads). * Step Time Lambda 3000000 15000.00000 0.00000 Energies (kJ/mol) Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR) 1.79026e+03 3.51875e+03 6.09547e+02 4.97912e+03 0.00000e+00 Potential Kinetic En. Total Energy Temperature Pressure (bar) 1.08977e+04 5.78924e+03 1.66869e+04 4.84033e+02 3.57640e+03Not all bonded interactions have been properly assigned to the domain decomposition cellsA list of missing interactions: Tab. Bonds of 880 missing 1 Tab. Angles of 800 missing 3 Tab. Dih. of 560 missing 4Molecule type 'POLCAR'the first 10 missing interactions, except for exclusions: Tab. Dih. atoms 2 3 4 5 global 566 567 568 569 Tab. Angles atoms 3 4 5 global 567 568 569 Tab. Dih. atoms 3 4 5 6 global 567 568 569 570 Tab. Angles atoms 4 5 6 global 568 569 570 Tab. Dih. atoms 4 5 6 7 global 568 569 570 571 Tab. Bonds atoms 5 6 global 569 570 Tab. Angles atoms 5 6 7 global 569 570 571 Tab. Dih. atoms 5 6 7 8 global 569 570 571 572-------------------------------------------------------Program mdrun_463, VERSION 4.6.3Source code file: /tmp/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393 Fatal error:8 of the 2240 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 GROMACSwebsite at http://www.gromacs.org/Documentation/Errors <http://www.gromacs.org/Documentation/Errors>-------------------------------------------------------* I do not understand the origin of problem. Can any one suggest how do the dihedrals should be taken care? Chandan On Wed, Dec 11, 2013 at 1:26 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > Agreed. I would suggest varying which of the tables are used, to find a > culprit. > > Mark > On Dec 11, 2013 1:46 AM, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On Tue, Dec 10, 2013 at 4:47 AM, Chandan Choudhury <iitd...@gmail.com > > >wrote: > > > > > On Mon, Dec 9, 2013 at 8:20 PM, Chandan Choudhury <iitd...@gmail.com> > > > wrote: > > > > > > > > > > > > > > > On Mon, Dec 9, 2013 at 6:46 PM, Justin Lemkul <jalem...@vt.edu> > wrote: > > > > > > > >> > > > >> > > > >> On 12/9/13 8:09 AM, Chandan Choudhury wrote: > > > >> > > > >>> On Mon, Dec 9, 2013 at 5:41 PM, Mark Abraham < > > mark.j.abra...@gmail.com > > > > > > > >>> wrote: > > > >>> > > > >>> Do your tabulated functions work on a toy system, like butane? > > > >>>> > > > >>>> No Mark. I didnot try with butane. The simulation stops when I > > > >>> incorporated > > > >>> tabulated dihedral potential. > > > >>> > > > >>> > > > >> Which is precisely why Mark is suggesting that you test something > > > simple. > > > >> If the simulation runs using a normal potential, but fails with > your > > > >> tabulated potential, that suggests quite strongly that your > tabulated > > > >> potential is not sound. So you need to go back to something very > > simple > > > >> that should have a very obvious outcome and scrutinize its success > or > > > >> failure, then move on to something slightly more complex, etc until > it > > > >> fails and you identify where the problem lies. > > > >> > > > > > > > > Thanks for the reply. > > > > > > > > Initially the system had 80 chains. Now I reduced it to single chain. > > The > > > > single chains consisted of just 12 Coarse Grained beads. > > > > The simulation proceeds very smoothly for 200000000 steps. > > > > The tabulated bond, tab. angle and tab. dihedral potentials were on. > > > > > > > > Few more updates. > > > I now increased the no. of chains to 10. The system now consists of 120 > > > beads. Will all the tabulated potentials, following is the snippet form > > the > > > log file: > > > > > > > > > > > > Step Time Lambda > > > 77670000 388350.00000 0.00000 > > > > > > Energies (kJ/mol) > > > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb > > (SR) > > > 2.03886e+02 5.00884e+02 1.33715e+02 9.77543e+01 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > > (bar) > > > 9.36239e+02 7.78233e+02 1.71447e+03 5.24366e+02 > > 6.92929e+01 > > > > > > Step Time Lambda > > > 77675000 388375.00000 0.00000 > > > > > > Energies (kJ/mol) > > > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb > > (SR) > > > nan 3.50433e+06 nan 0.00000e+00 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > > (bar) > > > nan -nan -nan -nan > > -nan > > > > > > Step Time Lambda > > > 77680000 388400.00000 0.00000 > > > > > > Energies (kJ/mol) > > > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb > > (SR) > > > nan 3.50433e+06 nan 0.00000e+00 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > > (bar) > > > nan -nan -nan -nan > > -nan > > > > > > Step Time Lambda > > > 77685000 388425.00000 0.00000 > > > > > > Energies (kJ/mol) > > > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb > > (SR) > > > nan 3.50433e+06 nan 0.00000e+00 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > > (bar) > > > nan -nan -nan -nan > > -nan > > > > > > ........ > > > ........ > > > Writing checkpoint, step 200000000 at Tue Dec 10 00:12:21 2013 > > > > > > > > > Energies (kJ/mol) > > > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb > > (SR) > > > nan 3.50433e+06 nan 0.00000e+00 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > > (bar) > > > nan -nan -nan -nan > > -nan > > > > > > <====== ############### ==> > > > <==== A V E R A G E S ====> > > > <== ############### ======> > > > > > > Statistics over 200000001 steps using 2000001 frames > > > > > > Energies (kJ/mol) > > > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb > > (SR) > > > nan 2.14355e+06 nan 3.19828e+01 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > > (bar) > > > nan -nan -nan -nan > > -nan > > > > > > Total Virial (kJ/mol) > > > -nan -nan -nan > > > -nan -nan -nan > > > -nan -nan -nan > > > > > > Pressure (bar) > > > -nan -nan -nan > > > -nan -nan -nan > > > -nan -nan -nan > > > > > > > > > Due the limitation in the no. of beads, the simulation runs on single > > > processor. The mdrun doesnot show any error. It proceeds upto 200000000 > > > steps. But we can see from the log file after 77675000 steps there is > > some > > > problem. > > > I also run a simulation with just 2 chains (24 beads). The simulation > > > proceeds smoothly. Output of log file: > > > > > > 199995000 999975.00000 0.00000 > > > > > > Energies (kJ/mol) > > > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb > > (SR) > > > 2.01529e+01 8.50365e+01 1.34663e+01 1.44338e+00 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > > (bar) > > > 1.20099e+02 1.92775e+02 3.12874e+02 6.72038e+02 > > 2.80949e+01 > > > > > > Step Time Lambda > > > 200000000 1000000.00000 0.00000 > > > > > > Writing checkpoint, step 200000000 at Tue Dec 10 15:10:21 2013 > > > > > > > > > Energies (kJ/mol) > > > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb > > (SR) > > > 2.50423e+01 1.12245e+02 1.85350e+01 2.55573e+00 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > > (bar) > > > 1.58378e+02 1.69571e+02 3.27949e+02 5.91148e+02 > > 6.65343e+00 > > > > > > <====== ############### ==> > > > <==== A V E R A G E S ====> > > > <== ############### ======> > > > > > > Statistics over 200000001 steps using 2000001 frames > > > > > > Energies (kJ/mol) > > > Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb > > (SR) > > > 4.48786e+01 8.97012e+01 2.00644e+01 2.34681e+00 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > > (bar) > > > 1.56991e+02 1.44750e+02 3.01741e+02 5.04619e+02 > > 1.54418e+00 > > > > > > Total Virial (kJ/mol) > > > 4.35571e+01 8.71257e-02 2.84028e-01 > > > 8.71252e-02 4.38582e+01 3.08832e-01 > > > 2.84028e-01 3.08832e-01 4.37737e+01 > > > > > > Pressure (bar) > > > 1.60808e+00 -2.94158e-02 -7.80104e-02 > > > -2.94156e-02 1.48653e+00 -1.01639e-01 > > > -7.80103e-02 -1.01639e-01 1.53793e+00 > > > > > > I donot understand what might be the problem. Is it actually the input > > > tabulated potentials or something else? > > > > > > > Still looks like the tabulated potential is the problem. Increasing the > > number of chains simply increases the likelihood of one or more > > interactions to fail. > > > > -Justin > > > > -- > > > > ========================================== > > > > Justin A. Lemkul, Ph.D. > > Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 601 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > > > ========================================== > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Chandan kumar Choudhury NCL, Pune INDIA -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.