openmm
Does the CHARMM36 force field include the CHARMM36m modifications?
Would someone be able to tell me whether the CHARMM36 force field in openmmforcefields contains the CHARMM36m revision (https://doi.org/10.1038/nmeth.4067)?
I'm trying to piece together information from the repo and http://mackerell.umaryland.edu/charmm_ff.shtml but struggling to reach a firm conclusion.
If it doesn't, does anyone know where I can get CHARMM36m in OpenMM XML format?
@jgreener64 : Apologies for not being able to respond to this earlier.
Information on the CHARMM force field currently available through openmmforcefields can be found here:
https://github.com/openmm/openmmforcefields/tree/main/charmm
It looks like the last time we updated this was from toppar_c36_jul20.tgz, and the complete list of files processed is listed in our charmm36.yaml.
The MacKerell lab is now providing toppar_c36_jul22.tgz, so we should probably regenerate these for this update. This presents us with a good opportunity to also add the CHARMM36m force field as well.
We don't have experience with these force fields, so if you could give us guidance in how we should modify our charmm36.yaml to generate a CHARMM36m variant, that would be helpful!
In the original toppar_c36_ul20.tgz file, I find these filenames containing 36m:
toppar_c36_jul20/stream/prot/toppar_all36_prot_c36m_d_aminoacids.str
toppar_c36_jul20/par_all36m_prot.prm
Do these files replace their non-m suffixed equivalents?
I also have limited experience with these force fields, but yes I believe that the m suffixed files replace the non-m suffixed equivalents for those two files.
In fact in toppar_c36_jul22.tgz the non-m suffixed equivalents are removed, i.e. CHARMM36m seems to be the default.
Is there any update on this? I'm also looking to use CHARMM36m with OpenMM, a possible workaround is to use the CHARMM/GMX setup tools and use this with OpenMM, but it would be nice to directly use the xml format
Is there will be update in the future? I want to directly use the xml format for the toppar_c36_jul22.tgz.
+1 Being able to easily swap between the force fields would be very convenient and appreciated!
I downloaded the par_all36m_prot.prm in the July 2020 version from http://mackerell.umaryland.edu/charmm_ff.shtml#charmm. In the openmm forcefield file, charmm36_nowaters.xml, I found the file with relationship to CHARMM36m force field, toppar_all36_prot_c36m_d_aminoacids.str being loaded into the xml file. However, I didn't find par_all36m_prot.prm being loaded. Can you confirm or deny that the charmm36_nowaters.xml is using CHARMM36m? Is there an XML file I can use that runs the force field CHARMM36m and not CHARMM36?
The latest update of the CHARMM force field parameters (#356) is based on the July 2024 release of the CHARMM force field, which uses CHARMM36m.
