[gmx-users] simulation using tabulated dihedral potentials.

[Justin Lemkul]

On 12/27/13, 12:58 AM, Chandan Choudhury wrote:
> 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?
>

Without the tabulated dihedrals, the system runs.  With them, it crashes.  It 
seems quite evident to me that whatever potential you are attempting to apply is 
the direct cause of instability.  The dihedrals are either badly parametrized or 
incorrectly implemented, but the source of the problem at this point is clear.

-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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