Dear Mark<br><br>Many thanks for your responces.<br><br>Yes, of course I have seen that. But what I am asking is if when using <i><b>vdw-type=cut-off</b></i> the potential is shifted acoording to the following equation:<br>
<br>V<font size="1">LJ</font>=V(r)-V(r<font size="1">c</font>) for r<r<font size="1">c</font> <br><br>Regards, Chrysostomos<br><br><div class="gmail_quote">On Wed, Apr 11, 2012 at 1:01 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><div> </div><div> </div><span>On 11/04/12, <b>Chrisostomos Batistakis </b><<a href="mailto:tomyvanbatis@gmail.com" target="_blank">tomyvanbatis@gmail.com</a>> wrote:</span>
</div><div class="im"><blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite">Dear Mark<br><br>I have already checked both sections but I don't understand.. That's why I am asking for help :-)</blockquote>
<div> </div></div><div>Then you'll have seen that by construction the shifted potential is zero above the cutoff. The question of truncation does not arise.</div><span class="HOEnZb"><font color="#888888"><div> </div>
<div>Mark</div></font></span><div class="HOEnZb"><div class="h5"><div> </div><blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite">
<div>
<div class="gmail_quote">On Wed, Apr 11, 2012 at 12:18 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>
<div>
<div><span>On 11/04/12, <b>Chrisostomos Batistakis </b><<a href="mailto:tomyvanbatis@gmail.com" target="_blank">tomyvanbatis@gmail.com</a>> wrote:</span></div><blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite">
<div>Dear all<br><br>I am looking in the manual but I don't understand...<br><br>When using <b>vdw-type =cut-off</b> in the .mdp file, is the LJ potential only truncated in the cut-off distance r<font size="1">c</font>, or is it also shifted in order to avoid discontinuity when <font size="-0">r<font size="1">ij</font>=r<font size="1">c</font></font> ?<br>
<br>If no, how can I have a shifted and truncated LJ potential?</div></blockquote>
<div> </div></div></div><div>Please check out the manual. Sections 4.1 and 7.3.11 come to mind.</div><span><font color="#888888">
<div> </div><div>Mark </div></font></span><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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" target="_blank">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote></div><br></div></blockquote>
<div> </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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>