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

[Thomas Piggot]

Hi Berk,

Thanks for the information, I just wanted to make sure that my message 
had not been missed.

Cheers

Tom

On 03/11/10 19:37, Berk Hess wrote:
> 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.
>
> Berk
>
> ------------------------------------------------------------------------
> 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
>
> Hi,
>
> 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.
>
> Berk
>
> > 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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-- 
Dr Thomas Piggot
University of Southampton, UK.

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