<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi,</div><div><br></div><div>all this has now been fixed I hope. The residues that I had missed are the ones my scripts not directly parse from the CHARMM ff files, i.e. they are hardcoded and hence I forgot to update the charge groups on them. Berk has now added an option of -1 to atoms added to terminals so that they become single charge groups as well, so that should be fine also. Let me know if I forgot something.</div><div><br></div><div>Regards,</div><div>Pär Bjelkmar</div><div><br></div><blockquote type="cite">Message: 2<br>Date: Wed, 3 Nov 2010 20:10:08 +0000<br>From: Thomas Piggot <<a href="mailto:t.piggot@soton.ac.uk">t.piggot@soton.ac.uk</a>><br>Subject: Re: [gmx-users] Single atom charge group implementation for<br><span class="Apple-tab-span" style="white-space: pre; "> </span>CHARMM27<span class="Apple-tab-span" style="white-space: pre; "> </span>in 4.5.2<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:4CD1C1A0.4060307@soton.ac.uk">4CD1C1A0.4060307@soton.ac.uk</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi Berk,<br><br>Thanks for the information, I just wanted to make sure that my message <br>had not been missed.<br><br>Cheers<br><br>Tom<br><br>On 03/11/10 19:37, Berk Hess wrote:<br><blockquote type="cite">I forgot to say that for the water models the rtp entries are only <br></blockquote><blockquote type="cite">used to recognize<br></blockquote><blockquote type="cite">the atoms. For the topology the itp files in the .ff dir are used.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Berk<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">------------------------------------------------------------------------<br></blockquote><blockquote type="cite">From: <a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a><br></blockquote><blockquote type="cite">To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite">Subject: RE: [gmx-users] Single atom charge group implementation for <br></blockquote><blockquote type="cite">CHARMM27 in 4.5.2<br></blockquote><blockquote type="cite">Date: Wed, 3 Nov 2010 20:32:58 +0100<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I saw your message, but I wanted to discuss with others before answering.<br></blockquote><blockquote type="cite">I have not had a chance for that yet, but I can answer anyhow.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">1. This is a mistake. The person converting the original Charmm files <br></blockquote><blockquote type="cite">edited his conversion<br></blockquote><blockquote type="cite">script, but the "special cases" can not be treated with this script. <br></blockquote><blockquote type="cite">We'll update them.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">2. Water is always a special case. It charge group is smaller than <br></blockquote><blockquote type="cite">most other charge<br></blockquote><blockquote type="cite">groups and force field independent. For performance reasons we don't <br></blockquote><blockquote type="cite">want to change this.<br></blockquote><blockquote type="cite">(although in a future release we might get rid of the complete charge <br></blockquote><blockquote type="cite">group concept)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">3. Termini charge groups were also overlooked. We can fix this. I <br></blockquote><blockquote type="cite">added support<br></blockquote><blockquote type="cite">for charge group numbers in the tdb file some time ago.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Berk<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Date: Wed, 3 Nov 2010 14:50:34 +0000<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">From: <a href="mailto:t.piggot@soton.ac.uk">t.piggot@soton.ac.uk</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Subject: [gmx-users] Single atom charge group implementation for <br></blockquote></blockquote><blockquote type="cite">CHARMM27 in 4.5.2<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Hi,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I sent this message a few days ago to the list but have not had a <br></blockquote></blockquote><blockquote type="cite">reply.<br></blockquote><blockquote type="cite"><blockquote type="cite">I feel some of the issues are quite important and so I am sending it <br></blockquote></blockquote><blockquote type="cite">again:<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I have a few questions/comments about the implementation of the single<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">atom charge groups with the CHARMM27 force field that maybe someone can<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">help with:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">1. There are some entries in aminoacids.rtp which have not been<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">converted to having every atom in a separate charge group (ASPP, CYS2,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">GLUP, LSN, HEME, HEO2, O2, C2 and HOH, hopefully I didn't miss any!). I<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">understand these are some of the less commonly used entries, have they<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">been left out for a reason? By the way I also noticed during a quick<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">test for this that there is not an rtp entry for ARGN but it is given as<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">an option by pdb2gmx when using -inter.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">2. Relating to 1 are the charge groups in the water models, which have<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">also been left as a water in a single charge group. I think I remember<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">reading somewhere that this is needed for the fast water loops in<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">GROMACS, so I assume this has been done on purpose. My concern is that<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">this is different to the TIP3P and TP3M entries in the aminoacids.rtp<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">file. If this has been done on purpose for the water models, then maybe<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">TIP3 and TP3M should also just have one charge group (as in the HOH <br></blockquote></blockquote><blockquote type="cite">entry)?<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">3. Finally, another concern I have is that when adding termini to a<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">protein (from aminoacids.c.tdb and aminoacids.n.tdb) then the terminal<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">atoms are still added as one charge group by pdb2gmx. I am not sure of a<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">way around this, apart from still using the -nochargegrp option, or<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">having AMBER forcefield style rtp entries for the N and C terminal<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">residues (undesirable I am sure).<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Cheers<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Tom<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On 30/10/10 20:56, Rossen Apostolov wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dear Gromacs users and developers,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">A new bugfix release of Gromacs is now available:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz">ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz</a>.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Here is a list of some of the resolved issues for 4.5.1:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* CHARMM force field now has single atom charge groups (pdb2gmx <br></blockquote></blockquote></blockquote><blockquote type="cite">-nochargegrp no longer required)<br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Made pdb2gmx -chainsep option work<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Fixed possible inconvenient npme node choice with pme load <br></blockquote></blockquote></blockquote><blockquote type="cite">between 0.33 and 0.50 which could lead to very slow mdrun performance.<br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Made Generalized Born gb_algorithm and sa_surface_tension active <br></blockquote></blockquote></blockquote><blockquote type="cite">and added a separate non-polar solvation term to the output.<br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Fixed issues in Generalized Born code that could cause incorrect <br></blockquote></blockquote></blockquote><blockquote type="cite">results with SSE and all-vs-all inner-loops.<br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Fixed bug with pressure coupling with nstlist=-1 that resulted <br></blockquote></blockquote></blockquote><blockquote type="cite">in extremely low densities.<br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Fixed corrupted energy and checkpoint file output with BAR free <br></blockquote></blockquote></blockquote><blockquote type="cite">energy calculations.<br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Fixed normalization of g_density using only the last frame.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Fixed several issues with cmake<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Several minor fixes.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Once again big thanks to all developers for their hard work, and <br></blockquote></blockquote></blockquote><blockquote type="cite">to all users for their contributions!<br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Happy simulating!<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Rossen<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dr Thomas Piggot<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">University of Southampton, UK.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Please search the archive at <br></blockquote></blockquote><blockquote type="cite"><a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br></blockquote><blockquote type="cite"><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a> Please search the <br></blockquote><blockquote type="cite">archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before <br></blockquote><blockquote type="cite">posting! Please don't post (un)subscribe requests to the list. Use the <br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>. 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