[gmx-users] question

[Justin Lemkul]

On 10/4/15 1:57 PM, Andrew Bostick wrote:
> Dear Justin,
>
> My previous problem was solved after I used all-bonds instead of hbonds in
> constraint section of mdp file. (I got the topology for my ligand using
> antechamber).
>
> After completion of NVT equilibration phase, I viewed nvt.gro using vmd.
>
> Please see the related figure in the following link:
>
> https://www.dropbox.com/s/i3ezsacp5jxotin/figure.png?dl=0
>
> What is the reason of this problem and how to resolve that?
>

No idea, but it looks from the snapshot like the ligand structure is very 
distorted.  Without access to coordinate files (before and after) and any 
relevant topologies, there's nothing useful or diagnostic that anyone can 
provide you.  Simply changing which bonds are constrained to "make it work" is 
not really a robust choice.  Some force fields should not be treated this way, 
for proper representation of dihedral rotations, etc.

-Justin

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

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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