I am trying to simulate a crystal too. I have a box size of .65 nm and
there are 8 bcc crystals in the system. Lattice parameter = 0.287 nm.<br>
<br>
I get a segmentation fault after mdrun -v. Is an atom with co-ordinates
0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system?
What I am trying to ask is, does GROMACS consider these as 2 different
atoms placed at the respective positions or do the 2 atoms overlap?<br>
<br>
What could be the reason for the segmentation fault? Is it because the atoms are too close to each other? <br>
-<br>
Karamyog.<br><br><div><span class="gmail_quote">On 5/23/06, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">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;">
David van der Spoel wrote:<br>> Gale, Ella wrote:<br>><br>>><br>>> Thanks for the advice, but my force-field has no charges and hence no<br>>> coulomb potential, so I want the atoms to interact with itself via the
<br>>> Van der Waals functions. I'm using 3.2.1 at the moment and there is no<br>>> option to use any of the Ewald summation techniques. Is this something<br>>> that has been added in the most recent version?
<br>><br>> Ewald variant are only for Coulomb so far. You can use a normal cutoff<br>> or a shifted cutoff.<br><br>One or two of the early PME papers describe implementation details for<br>LJ PME, but I am not immediately aware of a modern MD code that
<br>implements it. If you want it, shop around.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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