Vishal Agarwal wrote:
Dear Justin,
Thanks for replying. The table mentions only a few unit cell type. I am
using a monclinic unit cell. Do you know how these box vectors have been
derived.
Are you talking about your unit cell type, or the structure of the species you
wish to simulate? I see no mention of monoclinic box support in Gromacs, nor is
it listed as a type of box that can be defined with editconf, so you need to
clarify what it is you're trying to do. In any case, the last line of the .gro
file corresponds to the box vectors of the unit cell you specify with editconf.
If you don't specify anything explicitly, the default is to build a triclinic
unit cell.
-Justin
thanks
vishal
On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Vishal Agarwal wrote:
Dear gmx-users,
I am new to GROMACS. Can anyone tell me what does the last line
in .gro file stands for ?
The manual mentions
"box[X][X],box[Y][Y],box[Z][Z],
box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"
Can anyone explain what each of these mean in terms of cell
parameters ?
The last line contains the box vectors. Specifics in terms of unit
cell geometry are given in the manual, Table 3.1 and section 3.2.1.
-Justin
Thanks,
vishal
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Regards
***********************************************
Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
***********************************************
'Your only obligation in any lifetime is to be true to yourself."
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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