[gmx-users] periodic_molecule & missing interactions

[Justin Lemkul]

On 8/29/13 8:44 AM, Valentina wrote:
> I have a layered double hydroxide structure: i.e a sheet with Metals (Al &
> Mg), that are balanced by OH groups on both sides.
>
> The sheet should be periodic in xy-direction and there are bonds between Al
> and OH.
>
> For this, obv., I am using in-house FF, that I assign with pdb2gmx.
> In the molecule.rtp I specify bonds (Al-O, O-H) and angles (Al-O-H). There
> are no dihedrals, hence nrexcl is set to 2. I also have LJ and Coulomb.
>
> I run energy minimisation on a small cell containing 2 layers of mineral (
> 1.25680  x  1.08842 x 3.20000  + angles) and get an error on 32nd step.
>
> May be cell is too small?
>

Possibly.  What are your cutoffs?  I would imagine that unit cell violates the 
minimum image convention for all but the smallest cutoffs.  I don't know what 
your custom force field requires, though.

First, make your life easy.  Run with a single layer to make sure that's stable 
before adding a second layer.

-Justin

> When I run without periodic_molecule = yes I do not have such issue.
>
>
> Any help will be great!
>
>
> Step=   31, Dmax= 9.9e-02 nm, Epot=  1.95744e+08 Fmax= 3.13311e+06, atom= 64
>
> step 32: Water molecule starting at atom 404 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Step=   32, Dmax= 1.2e-01 nm, Epot=  1.95737e+08 Fmax= 8.74156e+05, atom=
> 404
> Step=   33, Dmax= 1.4e-01 nm, Epot=  1.95706e+08 Fmax= 2.39047e+05, atom= 50
>
> A list of missing interactions:
>                  Bond of    112 missing      4
>                 Angle of    168 missing     18
>            exclusions of    535 missing      8
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: domdec_top.c, line: 173
>
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "They Were So Quiet About It" (Pixies)
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-missing-interactions-tp5010815.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
==================================================

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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