[gmx-users] CHARMM FF

Nicolas Sapay nsapay at ucalgary.ca
Mon Aug 18 18:30:56 CEST 2008

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 <nsapay at ucalgary.ca 
> <mailto:nsapay at ucalgary.ca>> 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.


> Roland
> -- 
> Center for Molecular Biophysics ORNL/UT cmb.ornl.gov <http://cmb.ornl.gov>
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
A non-text attachment was scrubbed...
Name: nsapay.vcf
Type: text/x-vcard
Size: 282 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080818/eb63c3f0/attachment.vcf>

More information about the gromacs.org_gmx-users mailing list