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

[Thomas Piggot]

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.