[gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2
gmx3 at hotmail.com
Wed Nov 3 20:37:14 CET 2010
I forgot to say that for the water models the rtp entries are only used to recognize
the atoms. For the topology the itp files in the .ff dir are used.
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2
Date: Wed, 3 Nov 2010 20:32:58 +0100
I saw your message, but I wanted to discuss with others before answering.
I have not had a chance for that yet, but I can answer anyhow.
1. This is a mistake. The person converting the original Charmm files edited his conversion
script, but the "special cases" can not be treated with this script. We'll update them.
2. Water is always a special case. It charge group is smaller than most other charge
groups and force field independent. For performance reasons we don't want to change this.
(although in a future release we might get rid of the complete charge group concept)
3. Termini charge groups were also overlooked. We can fix this. I added support
for charge group numbers in the tdb file some time ago.
> Date: Wed, 3 Nov 2010 14:50:34 +0000
> From: t.piggot at soton.ac.uk
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2
> I sent this message a few days ago to the list but have not had a reply.
> I feel some of the issues are quite important and so I am sending it again:
> I have a few questions/comments about the implementation of the single
> atom charge groups with the CHARMM27 force field that maybe someone can
> help with:
> 1. There are some entries in aminoacids.rtp which have not been
> converted to having every atom in a separate charge group (ASPP, CYS2,
> GLUP, LSN, HEME, HEO2, O2, C2 and HOH, hopefully I didn't miss any!). I
> understand these are some of the less commonly used entries, have they
> been left out for a reason? By the way I also noticed during a quick
> test for this that there is not an rtp entry for ARGN but it is given as
> an option by pdb2gmx when using -inter.
> 2. Relating to 1 are the charge groups in the water models, which have
> also been left as a water in a single charge group. I think I remember
> reading somewhere that this is needed for the fast water loops in
> GROMACS, so I assume this has been done on purpose. My concern is that
> this is different to the TIP3P and TP3M entries in the aminoacids.rtp
> file. If this has been done on purpose for the water models, then maybe
> TIP3 and TP3M should also just have one charge group (as in the HOH entry)?
> 3. Finally, another concern I have is that when adding termini to a
> protein (from aminoacids.c.tdb and aminoacids.n.tdb) then the terminal
> atoms are still added as one charge group by pdb2gmx. I am not sure of a
> way around this, apart from still using the -nochargegrp option, or
> having AMBER forcefield style rtp entries for the N and C terminal
> residues (undesirable I am sure).
> On 30/10/10 20:56, Rossen Apostolov wrote:
> > Dear Gromacs users and developers,
> > A new bugfix release of Gromacs is now available:
> > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz.
> > Here is a list of some of the resolved issues for 4.5.1:
> > * CHARMM force field now has single atom charge groups (pdb2gmx -nochargegrp no longer required)
> > * Made pdb2gmx -chainsep option work
> > * Fixed possible inconvenient npme node choice with pme load between 0.33 and 0.50 which could lead to very slow mdrun performance.
> > * Made Generalized Born gb_algorithm and sa_surface_tension active and added a separate non-polar solvation term to the output.
> > * Fixed issues in Generalized Born code that could cause incorrect results with SSE and all-vs-all inner-loops.
> > * Fixed bug with pressure coupling with nstlist=-1 that resulted in extremely low densities.
> > * Fixed corrupted energy and checkpoint file output with BAR free energy calculations.
> > * Fixed normalization of g_density using only the last frame.
> > * Fixed several issues with cmake
> > * Several minor fixes.
> > Once again big thanks to all developers for their hard work, and to all users for their contributions!
> > Happy simulating!
> > Rossen
> Dr Thomas Piggot
> University of Southampton, UK.
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