[gmx-users] Docked ligand, umbrella sampling and "aiming"

[Justin Lemkul]

On 3/6/15 3:21 AM, Jernej Zidar wrote:
> Edit:
>    I tried to use the pull-geometry=direction and pull-vec but the latter
> option doesn't work:
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
>
> WARNING 1 [file md-pull-tune.mdp, line 69]:
>
>    Unknown left-hand 'pull-vec' in parameter file
> - - -
>
>    The relevant part of the md-pull-tune.mdp is:
>
> pull            = umbrella
> pull-geometry   = direction
> pull-vec = 1 0.5 0
> pull-start      = yes       ; define initial COM distance > 0
> pull-ngroups    = 2 ; number of groups involved in the pull
> pull-ncoords    = 1 ; number of reaction coordinates
> pull-coord1-groups = 1 2
> pull-group1-name = Protein
> pull-group2-name = BPA
> pull-coord1-rate      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull-coord1-k         = 1000      ; kJ mol^-1 nm^-2
>
>    The relevant section of the manual just mentions the "pull-vec"
> option withou elaborating much on it:
> http://manual.gromacs.org/online/mdp_opt.html#pull
>

Any reference to pull-vec is a typo and a relic of previous versions.  Scroll 
down past pull-geometry and you will see pull-coord-vec1, which is the 
equivalent of pull-vec.

-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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