[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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