<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Thanks for the info, I can stop trying :))<div><br></div><div>This is indeed a very useful option and hopefully easy to </div><div>implement.</div><div><br></div><div>XAvier.</div><div><br></div><div><div><div><div>On Mar 11, 2010, at 5:07 PM, Berk Hess wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Hi,<br><br>GMX 3 called cpp, GMX 4 uses its own cpp. I guess gmxcpp does not support this.<br>This is indeed a useful feature.<br>I have cc'ed David to ask if he can implement this.<br><br>Berk<br><br>> From:<span class="Apple-converted-space"> </span><a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a><br>> To:<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Date: Thu, 11 Mar 2010 17:00:33 +0100<br>> Subject: [gmx-users] defining value in the mdp file<br>><span class="Apple-converted-space"> </span><br>><span class="Apple-converted-space"> </span><br>> Dears,<br>><span class="Apple-converted-space"> </span><br>> I used to define values in the mdp file that are used in the<span class="Apple-converted-space"> </span><br>> topology. See below<br>> for an example. This is a way to easily make changes in the topology.<br>><span class="Apple-converted-space"> </span><br>> This was perfectly working in gmx331/333 but is not working anymore in<span class="Apple-converted-space"> </span><br>> gmx407.<br>> The value is clearly not passed along when processing the topology<span class="Apple-converted-space"> </span><br>> with grompp.<br>><span class="Apple-converted-space"> </span><br>> Typically if the "value" is used in the reference value of a bond<span class="Apple-converted-space"> </span><br>> definition I get the<br>> classic error message that there is no default value for the bond.<br>><span class="Apple-converted-space"> </span><br>> I can't understand where the problem comes from.<br>><span class="Apple-converted-space"> </span><br>> I run both gmx version on the same computer in case it matters.<br>><span class="Apple-converted-space"> </span><br>> Any suggestion would be appreciated.<br>><span class="Apple-converted-space"> </span><br>> XAvier.<br>><span class="Apple-converted-space"> </span><br>> exemple of use:<br>><span class="Apple-converted-space"> </span><br>> in the mdp file:<br>> define = -DRR=6.0<br>><span class="Apple-converted-space"> </span><br>> in the topology:<br>> [ bonds ]<br>> ...<br>> 200 204 1 RR 5000<br>> ...<br>><span class="Apple-converted-space"> </span><br>><span class="Apple-converted-space"> </span><br>> --<span class="Apple-converted-space"> </span><br>> gmx-users mailing list<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>><span class="Apple-converted-space"> </span><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>> www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><hr>New Windows 7: Find the right PC for you.<span class="Apple-converted-space"> </span><a href="http://windows.microsoft.com/shop" target="_new">Learn more.</a><span class="Apple-converted-space"> </span>--<span class="Apple-converted-space"> </span><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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></div></div></body></html>