CHARMM_scripts

These files can be used to prepare a protein ligand complex including crystal waters for CHARMM. Then the complexed systems can be solvated, neutralized, minimized, heated. After that MD simulations can be run either with NAMD or CHARMM (including openMM, BLaDE or domdec_gpu).

Note: water.crd is equilibrated water layer obtained from: https://www.charmm.org/wiki//index.php/CHARMM_Tutorial

For someone not familiar with CHARMM, I think the two important files/directories are:
tutorials and charmm_tutorial_2010.pdf

Contributors

MSLD and ALF feature Tracking

Update	Linear ALF	Nonlinear ALF	Reference
G_imp	Standard files	New files with theta bias	-
Theta bias	supported but will require updating the G_imp files	By default supported but if not required then change lmalf/src/lmalf.cu and also remove the theta bias from internal G_imp generation => Ryan	10.1021/acs.jctc.4c00514

Restraints and Engine compatability

Restraint	Domdec	BLaDE	OpenMM
NOE	Supported	Supported	No
MMFP	on CPU	only pair of atoms (Boresch type supported)	Some by Charlie and Argo
RESD	-	-	Supported
IC	-	-	-
RMSD	No	No	No
Cons Harm	Supported	No	didn't test
CATS	Supported	Supported	Not sure

Soft-core potentials and other FF related stuff

Feature	Domdec	BLaDE	OpenMM
non-integer e14fac	Supported	Supported	Supported
Geometric combination rules	Supported	Supported	ask Charlie
Periodic type improper torsions (eg. AMBER)	-	Supported	-
Soft Core	soft on	soft on	somm
Double exponential potential	-	-	-

Mixing force fields:

CHARMM/OPLS
Things to look for:
Combination rules : this can be taken care of by using either scalar or NBFIX (as I understand the role of NBFIX is to override the standard arithmetic combination rule for a selected atom pair, for more information see:10.1021/jp401512z)
e14fac = according to Charlie, there is no rationale as to why the interactions are scaled down (at least that’s what I understood) can be taken care of by using the scalar command (scalar e14fac set 0.5/1/0 select xxx end)