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View Code? Open in Web Editor NEWA tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
Home Page: https://doi.org/10.33011/livecoms.5.1.2067
A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
Home Page: https://doi.org/10.33011/livecoms.5.1.2067
Line 48 in bef7630
outputEnergies
should be outputenergy
np.mean should have been np.sum for error accumulation.
Some variable names are reused in the notebook. Those should be changed to avoid mismatched analysis (especially if the user isn't running everything sequentially).
We need to clarify that these lines are essential:
colvars on
colvarsConfig $CVconfig
But this line can be removed if the user doesn't have protein restraints:
cv configfile ../../common/protein_tilt.colvars
In the branch colvarsIssue, stepD input/run.namd
#############################################################
COLVARS
#############################################################
colvars on
if {$useSampleFiles} {
colvarsConfig ../../stepA_create_DBC/sample_outputs/DBC_restraint.colvars
} else {
colvarsConfig ../../stepA_create_DBC/outputs/DBC_restraint.colvars
}
cv configfile ../../common/protein_tilt.colvars#############################################################
FEP PARAMETERS
#############################################################
source ../../common/fep.tcl
alch on
alchType FEP
results in the error:
TCL: Setting parameter alch to on
FATAL ERROR: Alchemy must be enabled at startup to disable and re-enable in script.
FATAL ERROR: Alchemy must be enabled at startup to disable and re-enable in script.
[Partition 0][Node 0] End of program
BUT commenting out "cv configfile ..." runs normally (but without the Colvars defined in protein_tilt.colvars.
I'm already starting on this in refactorTI here and alternativeTI on the safep repo.
The notebook currently exposes a lot of nitty gritty code to the user which should be encapsulated and (eventually) moved to the safep package.
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