Vishal Agarwal wrote:
Dear Justin,
I am trying to set up calculations for a cellulose structure. The
allomorph of cellulose which I want to study has a monoclinic structure.
I have a .cif file of the XRD structure. I think the better question to
ask is how can I make input files using that.
That is a far more complex question. There are numerous posts in the list
archive regarding preparing input for polymeric systems, so please do search the
list archive. I helped one user set up a polyethylene system some time ago, so
that may help out. You'll have to familiarize yourself with .rtp entry
construction, specbond.dat (maybe), and the ins and outs of pdb2gmx to get it to
work though. There are lots of resources in the manual and on the Gromacs wiki
pages to get you started.
-Justin
thanks
vishal
On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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>
<mailto: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> <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."
---Richard Bach
--
========================================
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."
---Richard Bach
--
========================================
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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