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Hi Berk,<br>
<br>
Thanks for the information, I just wanted to make sure that my message
had not been missed.<br>
<br>
Cheers<br>
<br>
Tom <br>
<br>
On 03/11/10 19:37, Berk Hess wrote:
<blockquote cite="mid:COL113-W13F05C7D0CA0AA6B92EF68E4A0@phx.gbl"
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forgot to say that for the water models the rtp entries are only used
to recognize<br>
the atoms. For the topology the itp files in the .ff dir are used.<br>
<br>
Berk<br>
<br>
<hr id="stopSpelling">From: <a class="moz-txt-link-abbreviated" href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a><br>
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: RE: [gmx-users] Single atom charge group implementation for
CHARMM27 in 4.5.2<br>
Date: Wed, 3 Nov 2010 20:32:58 +0100<br>
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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: <a class="moz-txt-link-abbreviated" href="mailto:t.piggot@soton.ac.uk">t.piggot@soton.ac.uk</a><br>
> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><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>
> > <a class="moz-txt-link-freetext" href="ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz">ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz</a>.<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>
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<br>
<pre class="moz-signature" cols="72">--
Dr Thomas Piggot
University of Southampton, UK.
</pre>
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