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

[Sajeewa Pemasinghe]

Hi Justin,

I am really sorry for taking your time. I found my mistake. Earlier this
error was not there because I was applying my umbrella potential along x
axis only which has almost 120 A. Now I am applying umbrella potential
along both x and y axes. That is causing the problem as the y axis
dimension is not big enough. I will have to equilibrate the system in a
bigger box with a larger y dimension and run the umbrella sampling.

Thank you very much for your time.

Best,

Sajeewa

On Wed, Mar 29, 2017 at 11:26 PM, Sajeewa Pemasinghe <sajeewasp at gmail.com>
wrote:

> 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"
>>>>> 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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>>>
>>>
>>
>