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

[Sajeewa Pemasinghe]

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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