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.
