<DIV> </DIV><DIV> </DIV><SPAN>On 11/04/12, <B class=name>Chrisostomos Batistakis </B><tomyvanbatis@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CANUMDh_a2nAo3gMCZ=MKm+C=jCTw+uvuv8Y7+w=vgjvJMj0E-Q@mail.gmail.com type="cite">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> </BLOCKQUOTE>
<DIV> </DIV><DIV>No. It's cut off - discontinuous and probably fattening. It's equation 4.23 with r_1 = r_c </DIV><DIV> </DIV><DIV>Mark </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CANUMDh_a2nAo3gMCZ=MKm+C=jCTw+uvuv8Y7+w=vgjvJMj0E-Q@mail.gmail.com type="cite">
<DIV class="mimepart text html"><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 />
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<DIV> </DIV><DIV> </DIV><SPAN>On 11/04/12, <B>Chrisostomos Batistakis </B><<a href="mailto:tomyvanbatis@gmail.com" target=1 >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>
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<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=1 >mark.abraham@anu.edu.au</A>></SPAN> wrote:<br />
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<DIV><SPAN>On 11/04/12, <B>Chrisostomos Batistakis </B><<a href="mailto:tomyvanbatis@gmail.com" target=1 >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=1 >gmx-users@gromacs.org</A><br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=1 >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=1 >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=1 >gmx-users-request@gromacs.org</A>.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target=1 >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=1 >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=1 >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=1 >http://www.gromacs.org/Support/Mailing_Lists</A><br /></BLOCKQUOTE></DIV><br /></DIV></BLOCKQUOTE>
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