<html><body><div style="color:#000; background-color:#fff; font-family:garamond, new york, times, serif;font-size:14pt"><div id="yiv1953545210"><div><div style="color:#000;background-color:#fff;font-family:garamond, new york, times, serif;font-size:14pt;"><div id="yiv1953545210yui_3_2_0_268_132514519643548"><span id="yiv1953545210yui_3_2_0_268_132514519643579"><br></span><span></span></div><div><br id="yiv1953545210yui_3_2_0_268_132514519643551"></div> <div class="yiv1953545210yui_3_2_0_268_132514519643554" id="yiv1953545210yui_3_2_0_268_132514519643556" style="font-family:garamond, new york, times, serif;font-size:14pt;"> <div id="yiv1953545210yui_3_2_0_268_132514519643582" class="yiv1953545210yui_3_2_0_268_132514519643561" style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> "gmx-users-request@gromacs.org"
<gmx-users-request@gromacs.org><br> <b><span style="font-weight:bold;">To:</span></b> gmx-users@gromacs.org <br> <b><span style="font-weight:bold;">Sent:</span></b> Thursday, December 29, 2011 1:05 PM<br> <b><span style="
font-weight:bold;">Subject:</span></b> gmx-users Digest, Vol 92, Issue 138<br> </font> <br>
Send gmx-users mailing list submissions to<br> <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>or, via email, send a message with subject or body 'help' to<br> <a rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br><br>You can reach the person managing the list at<br> <a rel="nofollow" ymailto="mailto:gmx-users-owner@gromacs.org" target="_blank" href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's
Topics:<br><br> 1. Re: -pbc nojump (mohammad agha)<br> 2. positive potential energy (Zahra
M)<br> 3. Re: positive potential energy (Zahra M)<br> 4. Re: Re: positive potential energy (Mark Abraham)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Wed, 28 Dec 2011 18:54:54 -0800 (PST)<br>From: mohammad agha <<a rel="nofollow" ymailto="mailto:mra_bu@yahoo.com" target="_blank" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>><br>Subject: Re: [gmx-users] -pbc nojump<br>To: "<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a rel="nofollow" ymailto="mailto:1325127294.34356.YahooMailNeo@web125705.mail.ne1.yahoo.com" target="_blank"
href="mailto:1325127294.34356.YahooMailNeo@web125705.mail.ne1.yahoo.com">1325127294.34356.YahooMailNeo@web125705.mail.ne1.yahoo.com</a>><br>Content-Type: text/plain;
charset="us-ascii"<br><br>Thank you very much from your reply.<br><br>Best Regards<br>Sara<br><br><br>________________________________<br> From: Tsjerk Wassenaar <<a rel="nofollow" ymailto="mailto:tsjerkw@gmail.com" target="_blank" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>To: mohammad agha <<a rel="nofollow" ymailto="mailto:mra_bu@yahoo.com" target="_blank" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>>; Discussion list for GROMACS users <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <br>Sent: Thursday, December 29, 2011 1:56 AM<br>Subject: Re: [gmx-users] -pbc nojump<br> <br>Hi Sara,<br><br>Please keep discussions on the list. I'm not your private tutor.<br><br>Whether you can do your analysis depends on the analysis you want to<br>do. But if your aim is analyzing the formation of the micelle, you're<br>probably better of
reversing the trajectory.<br><br>> 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole
-s md.tpr<br><br>This makes molecules whole, which is fine. Clustering should make<br>molecules whole too, though, making this step redundant.<br><br>> 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 600000 -pbc cluster<br><br>Fine, you get a cluster<br><br>> 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro<br><br>This does nothing special. Just because you have a reference clustered<br>doesn't mean the output frame will turn out clustered.<br><br>> 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx<br>> 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc nojump<br><br>This screws up everything. You can only use -pbc nojump with a<br>reference structure that is sufficiently close to the first frame of<br>the trajectory. Your reference is a snapshot at t=600 ns.<br><br>> 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o<br>> cluster3.xtc<br><br>This would probably be
fine if the trajectory was okay there.<br><br>Cheers,<br><br>Tsjerk<br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20111228/d0b386d6/attachment-0001.html<br><br>------------------------------<br><br>Message: 2<br>Date: Thu, 29 Dec 2011 01:22:15 -0800 (PST)<br>From: Zahra M <<a rel="nofollow" ymailto="mailto:s_zahra_mousavi@yahoo.com" target="_blank" href="mailto:s_zahra_mousavi@yahoo.com">s_zahra_mousavi@yahoo.com</a>><br>Subject: [gmx-users] positive potential energy<br>To: "<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a rel="nofollow" ymailto="mailto:1325150535.62665.YahooMailNeo@web161705.mail.bf1.yahoo.com" target="_blank" href="mailto:1325150535.62665.YahooMailNeo@web161705.mail.bf1.yahoo.com">1325150535.62665.YahooMailNeo@web161705.mail.bf1.yahoo.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi dear all<br>I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: "The optimal PME mesh load for parallel simulations is below 0.5 and <br>for highly parallel simulations between 0.25 and 0.33, for higher <br>performance, increase the cut-off and the PME grid spacing", after running
grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my
results will be reasonable in this case or not, and how to solve that error.<br>thank you in advanced<br>Bests<br><br>-Zahra<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a rel="nofollow" target="_blank" href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20111229/d842ec1a/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20111229/d842ec1a/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 3<br>Date: Thu, 29 Dec 2011 01:24:14 -0800 (PST)<br>From: Zahra M <<a rel="nofollow" ymailto="mailto:s_zahra_mousavi@yahoo.com" target="_blank" href="mailto:s_zahra_mousavi@yahoo.com">s_zahra_mousavi@yahoo.com</a>><br>Subject: [gmx-users] Re: positive potential energy<br>To: "<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a rel="nofollow"
ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a rel="nofollow" ymailto="mailto:1325150654.64323.YahooMailNeo@web161705.mail.bf1.yahoo.com" target="_blank" href="mailto:1325150654.64323.YahooMailNeo@web161705.mail.bf1.yahoo.com">1325150654.64323.YahooMailNeo@web161705.mail.bf1.yahoo.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Sorry ...I forget to announce that my potential energy is positive, is it logical?<br><br><br><br>________________________________<br> From: Zahra M <<a rel="nofollow" ymailto="mailto:s_zahra_mousavi@yahoo.com" target="_blank" href="mailto:s_zahra_mousavi@yahoo.com">s_zahra_mousavi@yahoo.com</a>><br>To: "<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a rel="nofollow"
ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <br>Sent: Thursday, December 29, 2011 12:52 PM<br>Subject: positive potential
energy<br> <br><br>Hi dear all<br>I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: "The optimal PME mesh load for parallel simulations is below 0.5 and <br>for highly parallel simulations between 0.25 and 0.33, for higher <br>performance, increase the cut-off and the PME grid spacing", after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error.<br>thank you in advanced<br>Bests<br><br>-Zahra<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a rel="nofollow" target="_blank"
href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20111229/9a81cf29/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20111229/9a81cf29/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 4<br>Date: Thu, 29 Dec 2011 20:34:59 +1100<br>From: Mark Abraham <<a rel="nofollow" ymailto="mailto:Mark.Abraham@anu.edu.au" target="_blank" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] Re: positive potential energy<br>To: Discussion list for GROMACS users <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a rel="nofollow" ymailto="mailto:4EFC3443.8060301@anu.edu.au" target="_blank" href="mailto:4EFC3443.8060301@anu.edu.au">4EFC3443.8060301@anu.edu.au</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>On 29/12/2011 8:24
PM, Zahra M wrote:<br>> Sorry ...I forget to announce that my potential energy is positive, is <br>> it logical?<br><br>No.<br><br>><br>>
------------------------------------------------------------------------<br>> *From:* Zahra M <<a rel="nofollow" ymailto="mailto:s_zahra_mousavi@yahoo.com" target="_blank" href="mailto:s_zahra_mousavi@yahoo.com">s_zahra_mousavi@yahoo.com</a>><br>> *To:* "<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Thursday, December 29, 2011 12:52 PM<br>> *Subject:* positive potential energy<br>><br>> Hi dear all<br>> I'm simulating a system containing CNT, when I put CNT in a unit cell <br>> and want to run energy minimization in a vacuum, I encounter with such <br>> an error: "The optimal PME mesh load for parallel simulations is below <br>> 0.5 and for highly parallel simulations
between 0.25 and 0.33, for <br>> higher performance, increase the cut-off and the
PME grid spacing", <br>> after running grompp. I've tried a lot of numbers for cut-off radius <br>> ,but I didn't get any result, at last I changed the coulomb type from <br>> PME to Cut-off, and it worked, I want to know if my results will be <br>> reasonable in this case or not, and how to solve that error.<br><br>It's not an error, but an advisory about your performance, and doesn't <br>matter for EM in vacuo which will only run for a few seconds. Using a <br>plain cut-off is unreasonable by definition, but doesn't matter for EM <br>in vacuo. Otherwise, you should note that the suggestion is to "increase <br>the cut-off *and* the PME grid spacing," not just one of them.<br><br>Mark<br><br>Hi dear Mark<br>Thank you for your quick response.<br>I increased both of the grid spacing and cut-off, and it worked. <br>thank you very much...<br><br>-Zahra<br><br>> thank you in advanced<br>> Bests<br>><br>>
-Zahra<br>><br>><br>><br>><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a rel="nofollow" target="_blank" href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20111229/1a11eb72/attachment.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20111229/1a11eb72/attachment.html</a><br><br>------------------------------<br><br>-- <br>gmx-users mailing list<br><a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br><br>End of gmx-users Digest, Vol 92, Issue
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