[gmx-users] Free energy calculation using inter-molecular bonded interaction

[Justin Lemkul]

On 9/2/15 10:21 AM, Atsutoshi Okabe wrote:
> I mean that the entire [intermolecular_interaction] directive were commented out below;
> ;[ intermolecular-interactions ]
>
> ;[ bonds ]
> ;411 3173  6  0.55  2090
>
> ;[ angles ]
> ;411 3173 3152  1  164.5  20.9
> ;409 411 3173  1  122.3  20.9
>
> ;[ dihedrals ]
> ;409 411 3173 3152  2  12.0  20.9
> ;407 409 411 3173  2  75.6  20.9
> ;411 3173 3152 3144  2  -126.0  20.9
>
> I checked global atom number in .gro file of protein-ligand complex. It looks no problem.
> (407, 409 and 411 are atom number of protein,  3172, 3144 and 3152 are atom number of ligand in gro file of complex)
> Curiously, this error occurs when the vdW interaction between ligand and the environment becomes to turn-off(it means Lambda=0.7~1.0).
> Conversely, the calculations were finished normally when the vdW interaction remains(it means Lambda=0.0~0.7).
>

I've never tried using [bonds] in this context; the pull code is a better approach.

Perhaps there's an issue with the negative dihedral?  Have you tried turning 
these interactions on one-by-one to see if there is a specific entry that leads 
to a failure?  That's the most surefire way to find it.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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