[gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2

Berk Hess gmx3 at hotmail.com
Wed Nov 3 20:32:58 CET 2010


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
> Hi,
> 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).
> Cheers
> Tom
> 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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