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