Hi Periole, <br><br>May be this website is useful for implicit solvent calculations.<br><br><a href="http://apbs.sourceforge.net/">http://apbs.sourceforge.net/</a><br><br>mohan<br><br><div><span class="gmail_quote">On 17/04/06,
<b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Send gmx-users mailing list submissions to<br> <a 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://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>or, via email, send a message with subject or body 'help' to<br> <a 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 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: LINCS Warning with MDRUN - Segmentation Fault<br> (David van der Spoel)<br> 2. Re: Problems installing gromacs in a different directory<br> (David van der Spoel)<br> 3. Re: questions about implicit solvent simulation (
X.Periole)<br> 4. Re: LINCS Warning with MDRUN - Segmentation Fault (X.Periole)<br> 5. question on g_cluster (Osman Yogurtcu)<br> 6. Re: question on g_cluster (David van der Spoel)<br><br><br>----------------------------------------------------------------------
<br><br>Message: 1<br>Date: Mon, 17 Apr 2006 10:43:46 +0200<br>From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>Subject: Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault
<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:44435542.3090002@xray.bmc.uu.se">44435542.3090002@xray.bmc.uu.se</a>>
<br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Gaurav Chopra wrote:<br>> Hi<br>><br>> I am getting the following error with mdrun. I have done a few things<br>> but the system complains of 1-4 interactions and gives LINCS warning if
<br>> the constraints are not turned off in the mdp file. I also changed the<br>> fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I<br>> get 1-4 interaction table size error and then LINCS warning. The output
<br>> of mdrun for one of these peptides is as follows. I am working on normal<br>> mode decoys of each peptide and many of the decoys have no problems with<br>> mdrun but some gives this error and Segmentation Fault.
<br>><br>> Please advice.<br>><br>><br>you need to minimize better, but if your structures are really bad it<br>won't help either (e.g. when you have a sidechain sticking through a ring)<br><br>--<br>David.<br>
________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden
<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se
</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br><br>------------------------------<br><br>Message: 2<br>Date: Mon, 17 Apr 2006 10:42:14 +0200<br>From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a>><br>Subject: Re: [gmx-users] Problems installing gromacs in a different<br> directory<br>To: <a href="mailto:edumlopes@yahoo.com.br">edumlopes@yahoo.com.br</a>, Discussion list for GROMACS users
<br> <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:444354E6.3080509@xray.bmc.uu.se">444354E6.3080509@xray.bmc.uu.se</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
<br><br>Eduardo Martins Lopes wrote:<br>> Greetins fellow Gromacs Users, I come to thee because when I tried to<br>> install gromacs in a different directory without SU privileges I get the<br>> following error (the last few log lines)
<br>> Do I need super-user privileges ?<br>><br>> oppush.Tpo"; exit 1; fi<br>> if cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include<br>> -DGMXLIBDIR=\"/home/debora/gromacs/share/top\"<br>
> -I/home/debora/fftw/include -O3 -fomit-frame-pointer -finline-functions<br>> -Wall -Wno-unused -malign-double -funroll-all-loops -MT topcat.o -MD -MP<br>> -MF ".deps/topcat.Tpo" -c -o topcat.o topcat.c
; \<br>> then mv -f ".deps/topcat.Tpo" ".deps/topcat.Po"; else rm -f<br>> ".deps/topcat.Tpo"; exit 1; fi<br>> if cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include<br>> -DGMXLIBDIR=\"/home/debora/gromacs/share/top\"
<br>> -I/home/debora/fftw/include -O3 -fomit-frame-pointer -finline-functions<br>> -Wall -Wno-unused -malign-double -funroll-all-loops -MT topshake.o -MD<br>> -MP -MF ".deps/topshake.Tpo" -c -o topshake.o
topshake.c; \<br>> then mv -f ".deps/topshake.Tpo" ".deps/topshake.Po"; else rm -f<br>> ".deps/topshake.Tpo"; exit 1; fi<br>> make[2]: *** [all-recursive] Error 1<br>> make[2]: Leaving directory `/cluster/debora/gromacs-
3.3.1/src'<br>> make[1]: *** [all] Error 2<br>> make[1]: Leaving directory `/cluster/debora/gromacs-3.3.1/src'<br>> make: *** [all-recursive] Error 1<br>><br>><br>> FFTW was installed perfectly. Am I wrong or those files inside the
<br>> /gromacs-3.3.1/src are installed in the /src directory ? I have tried<br>> almost all combinations of fftw and gromacs and the same error is<br>> displayed everytime...<br>><br>> Thanks in advance<br>
><br>this works fine, I do it all the time.<br>Typically you should do<br>./configure --prefix=/home/joe/gromacs<br>or wherever you want it to go.<br><br><br>> Eduardo Martins Lopes<br>> Physics Student Universidade Federal de São Carlos - Brazil
<br>><br>> ------------------------------------------------------------------------<br>> Yahoo! Messenger com voz<br>> <<a href="http://us.rd.yahoo.com/mail/br/tagline/messenger/*http://br.messenger.yahoo.com/whatsnew.php">
http://us.rd.yahoo.com/mail/br/tagline/messenger/*http://br.messenger.yahoo.com/whatsnew.php</a>><br>> - Instale agora e faça ligações de graça.<br>><br>><br>> ------------------------------------------------------------------------
<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><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/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>--<br>David.<br>________________________________________________________________________
<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br><br><br>------------------------------<br><br>Message: 3<br>Date: Mon, 17 Apr 2006 10:49:09 +0200<br>From: "X.Periole" <<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>><br>Subject: Re: [gmx-users] questions about implicit solvent simulation
<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:web-19040600@mail3.rug.nl">web-19040600@mail3.rug.nl</a>><br>Content-Type: text/plain; charset="gb2312"; format="flowed"
<br><br><br>Dear Linchen,<br><br>As Mark already told you there is no implicit solvent<br>implementation in GROMACS ! The reaction field and<br>generalized reaction field options are corrections to the<br>long range electrostatic interactions.
<br>If you want to use an different dielectric cosntant than<br>one you have to specify it in the mdp file with the<br>keywork epsilon. Check out the manual for this, it must<br>be indicated.<br><br>> I want to do a implicit solvent MD simulation. I
<br>>wonder whether gromacs can fullfill the goal, if so,<br>>which option should I choose for electrostatics, reaction<br>>field or generalized reaction field? And what rcoulomb<br>>value is appropriate? if not, could I do a energy
<br>>minimization for my protein in an enviroment of<br>>dielectric constant other than 1?<br>> Thanks a lot for your attention:)<br>><br><br>XAvier<br><br><br>------------------------------<br><br>Message: 4
<br>Date: Mon, 17 Apr 2006 10:53:12 +0200<br>From: "X.Periole" <<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>><br>Subject: Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault<br>To: Discussion list for GROMACS users <
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:web-19040707@mail3.rug.nl">web-19040707@mail3.rug.nl</a>><br>Content-Type: text/plain; charset="ISO-8859-1"; format="flowed"
<br><br>On Mon, 17 Apr 2006 00:07:29 -0700<br> "Gaurav Chopra" <<a href="mailto:gauravchopra@gmail.com">gauravchopra@gmail.com</a>> wrote:<br>> Hi<br>><br>> I am getting the following error with mdrun. I have done
<br>>a few things but<br>> the system complains of 1-4 interactions and gives LINCS<br>>warning if the<br>> constraints are not turned off in the mdp file. I also<br>>changed the fudgeQQ =<br>> 1.0 (instead of
0.5) in ffoplsaa.itp and then did mdrun<br>>but I get 1-4<br>> interaction table size error and then LINCS warning. The<br>>output of mdrun for<br>> one of these peptides is as follows. I am working on<br>>normal mode decoys of
<br>> each peptide and many of the decoys have no problems<br>>with mdrun but some<br>> gives this error and Segmentation Fault.<br>><br>> Please advice.<br><br>The lincs warnning are on water molecules isn't it ???
<br><br>XAvier<br><br><br>------------------------------<br><br>Message: 5<br>Date: Mon, 17 Apr 2006 09:38:34 +0000 (GMT)<br>From: Osman Yogurtcu <<a href="mailto:karmatech@yahoo.co.uk">karmatech@yahoo.co.uk</a>><br>
Subject: [gmx-users] question on g_cluster<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:20060417093834.29692.qmail@web26302.mail.ukl.yahoo.com">20060417093834.29692.qmail@web26302.mail.ukl.yahoo.com
</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>Hi,<br><br>Is it possible to use g_cluster to cluster NAMD2 trajectories?<br><br>I am trying to use g_cluster to cluster my NAMD2 deriven trajectories. First, I converted my .dcd trajectory into .pdb format. Then, tried this:
<br><br>>g_cluster -f mypdb.pdb -cl clusters.pdb<br><br>and it did not work. Later, I converted my .pdb to .xtc and tried:<br><br>>g_cluster -f myxtc.xtc -cl clusters.pdb<br><br>does not work either. Should I include a Gromacs MD run specific .tpr topology file as well, though it is mentioned as "optional input"?
<br><br>I hope you can help me out,<br><br>Best<br><br>Osman N. Yogurtcu<br><br>Center for Computational Biology and Bioinformatics<br>Research Assistant<br>Koc University<br>-------------- next part --------------<br>An HTML attachment was scrubbed...
<br>URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20060417/ce5b3aa1/attachment-0001.html">http://www.gromacs.org/pipermail/gmx-users/attachments/20060417/ce5b3aa1/attachment-0001.html</a><br><br>------------------------------
<br><br>Message: 6<br>Date: Mon, 17 Apr 2006 11:52:07 +0200<br>From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>Subject: Re: [gmx-users] question on g_cluster<br>To: Osman Yogurtcu <
<a href="mailto:karmatech@yahoo.co.uk">karmatech@yahoo.co.uk</a>>, Discussion list for<br> GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:44436547.9070608@xray.bmc.uu.se">
44436547.9070608@xray.bmc.uu.se</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Osman Yogurtcu wrote:<br>> Hi,<br>><br>> Is it possible to use g_cluster to cluster NAMD2 trajectories?
<br>><br>> I am trying to use g_cluster to cluster my NAMD2 deriven trajectories.<br>> First, I converted my .dcd trajectory into .pdb format. Then, tried this:<br>><br>> >g_cluster -f mypdb.pdb -cl clusters.pdb
<br>><br>> and it did not work. Later, I converted my .pdb to .xtc and tried:<br>><br>> >g_cluster -f myxtc.xtc -cl clusters.pdb<br>><br>> does not work either. Should I include a Gromacs MD run specific .tpr
<br>> topology file as well, though it is mentioned as "optional input"?<br>><br>> I hope you can help me out,<br>><br><br><br>try using -s reference.pdb<br><br>> Best<br>><br>> Osman N. Yogurtcu
<br>> Center for Computational Biology and Bioinformatics<br>> Research Assistant<br>> Koc University<br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________
<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
<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/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br><br>------------------------------
<br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br><br><br>End of gmx-users Digest, Vol 24, Issue 55<br>*****************************************<br></blockquote></div><br><br clear="all"><br>-- <br>Mohan Boggara<br>Department of Chemical Engineering<br>University of Houston
<br>S222 Engineering Bldg 1<br>Houston, Texas-77204, USA<br>Mobile: 1-713-259-2166<br>Office: 1-713-743-4314 <br><a href="http://polymer.chee.uh.edu/">http://polymer.chee.uh.edu/</a><br><br>All human actions have one or more of these seven causes: chance, nature, compulsion, habit, reason, passion, and desire.-- Aristotle