[gmx-users] simulation using tabulated dihedral potentials.

Chandan Choudhury iitdckc at gmail.com
Fri Dec 27 06:58:41 CET 2013


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.abraham at 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" <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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--
Chandan kumar Choudhury
NCL, Pune
INDIA


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