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

Sajeewa Pemasinghe sajeewasp at gmail.com
Wed Mar 29 21:26:05 CEST 2017

So if the actual distance is 2.3 nm why does GROMACS measure it as 3.599998
nm ?

On Wed, Mar 29, 2017 at 11:11 PM, Sajeewa Pemasinghe <sajeewasp at gmail.com>
wrote:

> The coordinates of group1 center of mass are 44.466, 23.909,35.035 and
> that of group 2 are 67.467,23.994,34.088 as calculated in VMD . So the
> distance is 23 A .
>
> On Wed, Mar 29, 2017 at 11:05 PM, Sajeewa Pemasinghe <sajeewasp at gmail.com>
> wrote:
>
>> Hi Justin,
>>
>> Thank you for the prompt reply. I asked a second question correcting the
>> value of 23.0 nm. The distance value is 2.3 nm.
>>
>> On Wed, Mar 29, 2017 at 10:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> 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"
>>>>
>>>> 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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>>
>>
>