i think since i do not have cell as of now.. i.e with 0.5 0.5 0.5 cell
size and also with 1.0 1.0 1.0 cell size , gromacs is not able to
generate pbc.<br><br><div><span class="gmail_quote">On 5/11/06, <b class="gmail_sendername">Tsjerk Wassenaar</b> <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><br>Karam,<br><br>If you think you know why, please share your thoughts.. that can help us provide an answer.<br><br>Still,
gromacs supports all periodic boundary conditions, except for real
exotic stuff like spherical (and I can think of a few others). But any
crystal packing can be handled. Maybe the easiest for you is to build a
single bcc unit cell, with the correct lattice vectors as the box
definition. Then run genbox to copy that a certain number of times.
Also read the gromacs manual to understand the definition of the box
(last line of the .gro file) if you haven't done so.
<br></div><div><span class="sg"><br>Tsjerk<br><br></span></div><div><div></div><div><span class="q"><span class="gmail_quote">On 5/11/06, <b class="gmail_sendername">karamyog singh</b> <<a href="mailto:karamyog.singh@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
karamyog.singh@gmail.com</a>> wrote:</span></span></div><div><span class="e" id="q_10b23cb67b40155e_4"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>hmm.. i know about the no. of atoms in bcc. please tell me what to do if i want more than 1 unit cell?<br>gromacs is not supporting periodic boundary conditions for my cell and i think i know y.<br><div><span class="gmail_quote">
On 5/11/06, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">Mark.Abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
karamyog singh wrote:<br>> Thnx Mark. I stil have a doubt. If want to simulate a crystal<br>> structure,then how should i go about it? wht changes should be made in<br>> the above file? even if i replace the 27th atom with
0.5 0.25 0.5, then<br>> too it will overlay some other atom.<br><br>0.5 == 0 if the size is 0.5. If you've got the atom spacing right for 27<br>atoms in this configuration, then increase your box size to make the<br>periodic images go in the right spots. At the moment you are overlaying
<br>atoms.<br><br>> I understand wht the fault with my conf.gro file is, but if I have to<br>> simulate a bcc lattice then wht should the .gro file look like?<br><br>IIRC, a bcc lattice has two atoms per unit cell
e.g
. the central one and<br>eight eighths of an atom at each of the cube vertices. Thus I have no<br>idea what you're trying to do with 27 atoms.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list
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</a><br><br></blockquote></span></div><div></div><br><br clear="all"></div><div><span class="e" id="q_10b23cb67b40155e_6"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen
<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>
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