[gmx-users] simulation using tabulated dihedral potentials.

[Chandan Choudhury]

On Sat, Dec 28, 2013 at 5:24 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.


Thanks Justin for the response.
According to you dihedrals are badly parameterized or incorrectly
implemented.

A. I follow the Boltzmann inversion (BI) method to get the dihedral
potentials. I follow the steps outlined in VOTCA to obtain the tables. Here
are summarize what I did to obtain the dihedral tables:
1. Using BI method, I obtain the potential from distributions.
2. The potentials are then smoothed and extrapolated, as implemented in
VOTCA.
3. Then generate the tables.

I have uploaded the tables (along with necessary files) at
https://www.dropbox.com/s/yumzdufuys1ifdr/with-dih.tar.

B. If the tabulated dihedrals are incorrectly implemented, then can you
guide me how can this be checked and confirmed?
Guidance regarding this would be very helpful.

Chandan



>
>
> -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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