<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear ALL,</span></div><div><br><span></span></div><div><span> We could not run DSSP for analysing the secondary structure. Any help in this regard is very much appreciated<br></span></div><div><br><span></span></div><div><span></span></div><div> </div><div>*******************************+ <br>Dr.Karunakaran Chandran +<br>Biophysics Department + <br>Medical College of Wisconsin +<br>Milwaukee, WI-53226 +<br>Resi.: 414-443-0085 +<br>Off : 414-456-4034 +<br>********************************<br></div> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div dir="ltr"> <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> Monday, 19 March 2012 4:30 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> gmx-users Digest, Vol 95, Issue 125<br> </font> </div> <br>Send gmx-users mailing list submissions to<br> <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>or, via email, send a message with subject or body 'help' to<br> <a ymailto="mailto:gmx-users-request@gromacs.org"
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 ymailto="mailto:gmx-users-owner@gromacs.org" 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. Editing potential parameters (Asaf Farhi)<br> 2. nrexcl in topology (Lara Bunte)<br> 3. extending simulation (priya thiyagarajan)<br> 4. Re: nrexcl in topology (R.Perez Garcia)<br> 5. Re: Force constant - Umbrella Sampling (lloyd riggs)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Mon, 19 Mar 2012 10:06:47 +0000<br>From: Asaf Farhi <<a ymailto="mailto:asaf.farhi@weizmann.ac.il"
href="mailto:asaf.farhi@weizmann.ac.il">asaf.farhi@weizmann.ac.il</a>><br>Subject: [gmx-users] Editing potential parameters<br>To: "<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <7D02BCA1E8377E4AABC2E8F59B6D0CDA09E25B@IBWMBX01><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Dear Gromacs user<br><br>Hi. My name is Asaf and I'm trying to edit potential parameters for the non bonded interaction potential terms between specific atoms (k1 for 1 subset of pairs and k2 for anoother subset of pairs).<br>Is the pairs section in the topology file the correct place to do this? and if so how would you incorporate spring constant for particular pair interaction?<br><br>Many thanks.<br>Best regards,<br>Asaf<br>-------------- next part --------------<br>An HTML
attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/6adac179/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/6adac179/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 2<br>Date: Mon, 19 Mar 2012 10:19:22 +0000 (GMT)<br>From: Lara Bunte <<a ymailto="mailto:lara.bunte@yahoo.de" href="mailto:lara.bunte@yahoo.de">lara.bunte@yahoo.de</a>><br>Subject: [gmx-users] nrexcl in topology<br>To: "<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a ymailto="mailto:1332152362.73030.YahooMailNeo@web29401.mail.ird.yahoo.com"
href="mailto:1332152362.73030.YahooMailNeo@web29401.mail.ird.yahoo.com">1332152362.73030.YahooMailNeo@web29401.mail.ird.yahoo.com</a>><br>Content-Type: text/plain; charset=iso-8859-1<br><br>Hi<br><br>in a topology file in the section [ moleculetypes ] is standing<br><br>; nrexcl <br><br> 3<br><br>What do this mean?<br><br>Thanks for help<br>Greetings<br>Lara<br><br><br>------------------------------<br><br>Message: 3<br>Date: Mon, 19 Mar 2012 03:26:55 -0700<br>From: priya thiyagarajan <<a ymailto="mailto:priya.thiyagarajan09@gmail.com" href="mailto:priya.thiyagarajan09@gmail.com">priya.thiyagarajan09@gmail.com</a>><br>Subject: [gmx-users] extending simulation<br>To: <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:<br> <<a ymailto="mailto:CAEuVTxAiRNq6nDxPPKgG_S34ufzYZVg2Z2-BkoAucNQOK4FtMQ@mail.gmail.com"
href="mailto:CAEuVTxAiRNq6nDxPPKgG_S34ufzYZVg2Z2-BkoAucNQOK4FtMQ@mail.gmail.com">CAEuVTxAiRNq6nDxPPKgG_S34ufzYZVg2Z2-BkoAucNQOK4FtMQ@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>hello sir,,<br><br>initially i did my simulation for 10ns.. after getting result i analysed it<br>and thought of extending the simulation for another 10ns..<br><br>i used following commands..<br><br>tpbconv *-s md.tpr -o newmd.tpr -extend 10000.00*<br><br>*mdrun -s newmd.tpr -o md3_2.trr -c md_2.gro -e md_2.edr -g md_2.log -cpi<br>state1.cpt -noappend*<br><br><br>is it correct..<br><br>we ll use tpbconv to extend the simulation which terminated in the middle..<br><br>is it correct to use the same command for completed run...<br><br>please help me with your answer..<br><br>Thanking you sir,<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a
href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/9248f3aa/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/9248f3aa/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 4<br>Date: Mon, 19 Mar 2012 11:27:43 +0100<br>From: "R.Perez Garcia" <<a ymailto="mailto:r.perez.garcia@student.rug.nl" href="mailto:r.perez.garcia@student.rug.nl">r.perez.garcia@student.rug.nl</a>><br>Subject: Re: [gmx-users] nrexcl in topology<br>To: Lara Bunte <<a ymailto="mailto:lara.bunte@yahoo.de" href="mailto:lara.bunte@yahoo.de">lara.bunte@yahoo.de</a>>, "<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>"<br> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:7630868d774ff.4f67182f@rug.nl"
href="mailto:7630868d774ff.4f67182f@rug.nl">7630868d774ff.4f67182f@rug.nl</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br><a href="http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html</a><br><br>On 19-03-12, Lara Bunte <<a ymailto="mailto:lara.bunte@yahoo.de" href="mailto:lara.bunte@yahoo.de">lara.bunte@yahoo.de</a>> wrote:<br>> Hi<br>> <br>> in a topology file in the section [ moleculetypes ] is standing<br>> <br>> ; nrexcl <br>> <br>> 3<br>> <br>> What do this mean?<br>> <br>> Thanks for help<br>> Greetings<br>> Lara<br>> -- <br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" 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 ymailto="mailto:gmx-users-request@gromacs.org" 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>> <br>> <br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/00e8b769/attachment-0001.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/00e8b769/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 5<br>Date: Mon, 19 Mar 2012 11:43:49 +0100<br>From: "lloyd riggs" <<a ymailto="mailto:lloyd.riggs@gmx.ch" href="mailto:lloyd.riggs@gmx.ch">lloyd.riggs@gmx.ch</a>><br>Subject: Re: [gmx-users] Force constant - Umbrella Sampling<br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:20120319104349.106190@gmx.net" href="mailto:20120319104349.106190@gmx.net">20120319104349.106190@gmx.net</a>><br>Content-Type: text/plain; charset="utf-8"<br><br><br>>From liturature it ranges around 1K for unravling proteins, and protein-protein dissociations range around 2-3k (kj/mol that is). For small molecules I have no clue. Id like to know if
somone finds out ranges for any of these though....<br><br>Stephan Watkins <br><br>-------- Original-Nachricht --------<br>> Datum: Mon, 19 Mar 2012 08:48:15 +0000<br>> Von: Steven Neumann <<a ymailto="mailto:s.neumann08@gmail.com" href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>><br>> An: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>, <a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>> Betreff: [gmx-users] Force constant - Umbrella Sampling<br><br>> Dear Gmx Users, Dear Justin,<br>> <br>> As I saw in your tutorial you used the force of 1000 kJ/mol nm2 for the<br>> harmonic potential. You pulled the whole chain which is quite heavy. Would<br>> you decrease the force constant for a small molecule (app. 500 Da) during<br>> the umbrella sampling (e.g. 500 kJ/mol nm2) ? Is
it a guess or I should<br>> check calculations for e.g. 3 force constants and see the influence on the<br>> final binding free energy?<br>> <br>> Thank you,<br>> <br>> Steven<br><br>-- <br>NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! <br>Jetzt informieren: <a href="http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a" target="_blank">http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a</a><br><br><br>------------------------------<br><br>-- <br>gmx-users mailing list<br><a ymailto="mailto:gmx-users@gromacs.org" 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><br>End of gmx-users Digest, Vol 95, Issue 125<br>******************************************<br><br><br> </div> </div> </div></body></html>