[gmx-users] Box dimensions in the gro file are not read by GROMACS

[Justin Lemkul]

On 3/29/17 2:55 PM, Sajeewa Pemasinghe wrote:
> Hi everyone,
>
> I have run an equilibration of two linear molecules in a water box with
> dimensions 117A x 54A x 70A for 150 ns. I am using the equilibrated
> structures (not the final structure) in the final nanoseconds as starting
> structures for an umbrella sampling calculation. The problem is that as I
> only have a checkpoint (cpt) file for the final structure I have to start
> these umbrella sampling calculations without a cpt file. So my inputs to
> grompp are just the .gro files. During the umbrella sampling I get the
> following error
>
> Distance between pull groups 1 and 2 (3.599998 nm) is larger than 0.49
> times the box size (2.673675).
> You might want to consider using "pull-geometry = direction-periodic"
> instead.
>
> Although gromacs says that the distance between the pull groups 1 and 2 are
> 3.599998 nm, the actual distance in the snapshot is 23.0 nm. This was
> confirmed by calculating in vmd as well.
> The above error also says that the box size is 2.673675 nm. But at the
> bottom of the input gro file it shows the dimensions as 11.68645
> 5.34804   6.95245. So I cannot understand why it doesn't read those
> dimensions.
>

It is.  Half of 5.34804 is the value being reported in the error.  You also 
can't possibly have a distance of 23.0 nm if the longest box vector is half that 
value.

-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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