Sorry for the late answer. I wasn't in my office on the last 2 weeks.
Roland Schulz wrote:
On Thu, Jul 17, 2008 at 6:26 PM, Nicolas <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
We also have a implementation of CHARMM(27) for Gromacs, but
without CMAP as well.
How is it different to the one by Mark Abraham?
The CHARMM force field is the CHARMM force field, whatever the MD engine
you use or whoever done the implementation. For a same system, you must
obtain exactly the same energy values with CHARMM, NAMD or GROMACS (in
the NVE ensemble with full non-bonded interactions). In my case, I have
implemented pretty much all CHARMM27 compounds (amino acids, lipids,
nucleotides, etc) plus few CHARMM derived lipids with united atoms for
the acyl chains. I've got also a bunch of script to convert
home-developped CHARMM files into GROMACS files (useful, if you have
developed your own parameters for a Zn finger, e.g.).
Is it publicly available?
Not yet. As soon as the publication is accepted, I will put all the
scripts and files on the web (i.e. soon hopefully).
The main limitation is the computational cost due to the CHARMM
TIP3P water model (it cannot be treated by the special code
dedicated to water). IIRW the Gromacs 4 publication, the authors
said there is no particular to difficulty to makes the water loop
working for CHARMM TIP3P... Is it planed to implement that into
the CVS version?
The consensus on the CHARMM forum seems to be that this additional LJ
parameters are insignificant:
http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Number=1680&an=0&page=59
<http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Number=1680&an=0&page=59>
http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Number=643&Main=265
<http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Number=643&Main=265>
According to this I would think one could just use the standard TIP3P,
but I have not compared it myself yet.
I was not able to get a clear justification for the addition of LJ
parameters on the hydrogens. The explanation seems to be lost in a
thesis written in the early 80's. So, I did some tests on lipids and I
observed a significant difference between CHARMM and regular TIP3P. I
guess it is related to the surface accessible solvent and the number of
H-bonds that can be created between the water and the solute. To my
opinion, CHARMM or regular TIP3P probably make little difference in the
case small compounds or peptides. For example, I'm quite sure the
hydration energy would be quasi the same.
Nico
Roland
--
Center for Molecular Biophysics ORNL/UT cmb.ornl.gov <http://cmb.ornl.gov>
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