The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about 31 A away from the closest water in the box. But if it is periodic, shouldn't there be waters near the dummy too?<br><br><div class="gmail_quote">
On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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">On 4/03/2010 11:30 AM, Dian Jiao wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Gromacs users,<br>
<br>
I was trying to compute minimum distance between groups in a cubic water<br>
box with g_mindist using periodic boundary condition. In order to test<br>
this, I added one more "atom" which is far away from any of the other<br>
atoms in the pdb file. The mindist between that atom and all the waters<br>
were computed. The output of g_mindist is 3.089281e+00. (the unit is nm,<br>
right?)<br>
</blockquote>
<br></div>
You haven't said how big your box is, or how far "far away" is, so we can't tell whether you think 3nm is too big, too small, etc.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The manual shows that pbc is one of the option of g_mindist, but isn't<br>
the default "yes"? I even tried with "-pbc" in the command, still did<br>
not work. Can anyone tell me how to turn on PBC in g_mindist?<br>
</blockquote>
<br></div>
See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.<div class="im"><br>
<br>
Mark<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
</div><div><div></div><div class="h5"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>