[gmx-users] simulation using tabulated dihedral potentials.
Mark Abraham
mark.j.abraham at gmail.com
Tue Dec 10 20:56:45 CET 2013
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" <jalemkul at vt.edu> wrote:
> On Tue, Dec 10, 2013 at 4:47 AM, Chandan Choudhury <iitdckc at gmail.com
> >wrote:
>
> > On Mon, Dec 9, 2013 at 8:20 PM, Chandan Choudhury <iitdckc at gmail.com>
> > wrote:
> >
> > >
> > >
> > > On Mon, Dec 9, 2013 at 6:46 PM, Justin Lemkul <jalemkul at 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.abraham at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
> ==========================================
> --
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