[gmx-users] simulation using tabulated dihedral potentials.

Justin Lemkul jalemkul at vt.edu
Tue Dec 10 14:51:01 CET 2013


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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