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

[Sajeewa Pemasinghe]

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"
>>> 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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>
>