Dear Justin,<br><br>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. <br>
<br>thanks<br>vishal<br><br><div class="gmail_quote">On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Vishal Agarwal wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin,<br>
<br>
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.<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
thanks<br>
vishal<div class="im"><br>
<br>
On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Vishal Agarwal wrote:<br>
<br>
Dear gmx-users,<br>
<br>
I am new to GROMACS. Can anyone tell me what does the last line<br>
in .gro file stands for ?<br>
<br>
The manual mentions<br>
"box[X][X],box[Y][Y],box[Z][Z],<br>
box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"<br>
<br>
Can anyone explain what each of these mean in terms of cell<br>
parameters ?<br>
<br>
<br>
The last line contains the box vectors. Specifics in terms of unit<br>
cell geometry are given in the manual, Table 3.1 and section 3.2.1.<br>
<br>
-Justin<br>
<br>
Thanks,<br>
vishal<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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-- <br>
Regards<br>
<br>
***********************************************<br>
Vishal Agarwal<br>
Research Scholar<br>
University of Massachusetts, Amherst<br>
***********************************************<br>
'Your only obligation in any lifetime is to be true to yourself."<br>
---Richard Bach<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Regards<br><br>***********************************************<br>Vishal Agarwal<br>Research Scholar<br>University of Massachusetts, Amherst<br>***********************************************<br>
'Your only obligation in any lifetime is to be true to yourself."<br> ---Richard Bach<br>