<div dir="ltr">Many Thanks Ehud!<br><br>I was certainly not aware of that and I'll check it now..<br><br>Amir<br><br><div class="gmail_quote">On Wed, Jul 28, 2010 at 6:22 PM, Ehud Schreiber <span dir="ltr"><<a href="mailto:schreib@compugen.co.il">schreib@compugen.co.il</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 link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi again,</span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Yes, you can simply specify sigma
and epsilon, but indeed in your case you do not want to do so but rather to
specify C_6 and C_{12} with the former being zero to avoid attraction.</span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Your .top file should include a
[ defaults ] section, perhaps through an #include of a .itp file. Perhaps yours
is in ffamber99.itp (I don’t have it installed so I can’t tell). In
this section there are 5 parameters; the second is a “combination rule”
which must equal 1 for the two numbers to represent indeed C_6 and C_{12} (see
table 5.3, eq. 5.1-5.4, and in page 112).</span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">In short, check whether the
second parameter in the [ defaults ] section of ffamber99.itp is 1, if not that’s
probably the problem. Of course, if you change this you’ll screw up all
the other parameters, so it seems you could either change the force field or
create your copy of the files with all the relevant LJ parameters changed to
the “combination rule”=1 convention.</span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span></p>
<div>
<div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0in 0in;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> Ehud Schreiber <br>
<b>Sent:</b> Wednesday, July 28, 2010 3:01 PM<br>
<b>To:</b> '<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>'<br>
<b>Subject:</b> RE: [nonbond_params] section , choice of parameters</span></p>
</div>
</div><div class="im">
<p class="MsoNormal"> </p>
<p class="MsoNormal">Hi Amir,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Are you sure you’re giving the parameters indeed as
C_6 and C_{12}? </p>
<p class="MsoNormal">According to the combination rule in the [ defaults ]
section, you may be giving the two parameters directly as sigma and epsilon;
sigma=0 (as well as epsilon=0) would give an identically zero potential . See
sections 5.3.3 and 5.7.1 in the manual (version 4.0).</p>
<p class="MsoNormal"> </p>
</div></div>
</div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<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<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">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></blockquote></div><br></div>