Additional atomic group pairs will be added to determine the residence time between the ligand and receptor. The atomic group pairs receptor_group_<n> and ligand_group_<n> must be defined in the index file (.ndx), e.g.
[ receptor_group_1 ]
1 2
[ ligand_group_1 ]
4 5
During the simulation, the distances between the center of mass (COM) of each pair will be calculated at every RAMD evaluation step.
If the average of all distances exceeds the parameter 'ramd-residence-dist,' a message will be logged in the simulation file.
==== RAMD ==== Residence time obtained after <x> steps.
This message will only printed once.
Two new MDP options will be integrated:
ramd-use-residence-dist
If 'yes', the residence time will be printed to the log file. The default value is 'no'.
ramd-residence-dist
Residence distance in nm. If the ligand is within this distance from the receptor, it is considered to be bound. The default value is 0.55 nm.
The COM distances for the residence time will be saved in the last columns of the xvg file using the -ramd flag.
Additional atomic group pairs will be added to determine the residence time between the ligand and receptor. The atomic group pairs
receptor_group_<n>andligand_group_<n>must be defined in the index file (.ndx), e.g.During the simulation, the distances between the center of mass (COM) of each pair will be calculated at every RAMD evaluation step. If the average of all distances exceeds the parameter 'ramd-residence-dist,' a message will be logged in the simulation file.
This message will only printed once.
Two new MDP options will be integrated:
ramd-use-residence-distIf 'yes', the residence time will be printed to the log file. The default value is 'no'.ramd-residence-distResidence distance in nm. If the ligand is within this distance from the receptor, it is considered to be bound. The default value is 0.55 nm.The COM distances for the residence time will be saved in the last columns of the xvg file using the
-ramdflag.