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? 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