mindist as the reaction coordinate in AWH

[Kimia Sinaeian]

Hi,

I’m running umbrella‐sampling simulations in GROMACS + PLUMED and using the minimum distance between an ice slab and a protein as my collective variable. However, when I enable detailed timers, the DISTANCES (mindist) action dominates the runtime:

PLUMED:                                               Cycles        Total      Average      Minimum      Maximum
PLUMED:                                                    1   159.607975   159.607975   159.607975   159.607975
PLUMED: 1 Prepare dependencies                          2001     0.001755     0.000001     0.000000     0.000008
PLUMED: 2 Sharing data                                  2001     1.372998     0.000686     0.000491     0.002649
PLUMED: 4 Calculating (forward loop)                    2001   157.427915     0.078675     0.077893     0.099239
PLUMED: 4A 3 mindist                                    2001   157.409271     0.078665     0.077884     0.099221
PLUMED: 5 Applying (backward loop)                      2001     0.550658     0.000275     0.000253     0.000748
PLUMED: 5A 2 mindist                                    2001     0.538994     0.000269     0.000247     0.000741

# plumed.dat 

 ice: GROUP ATOMS= 

C_alpha: GROUP ATOMS=

 # Define minimum distance reaction coordinate 

 mindist: DISTANCES GROUPA=C_alpha GROUPB=ice MIN={BETA=100.0} 

 RESTRAINT ARG=mindist.min AT=0.298 KAPPA=1000.0 

 PRINT ARG=mindist.min FILE=COLVAR STRIDE=1000 DEBUG DETAILED_TIMERS 

Questions:

1. Why is the DISTANCES action (mindist) so expensive in this setup?

2. Are there PLUMED parameters or flags to speed up minimum‐distance calculations?

3. Any best practices for umbrella sampling with many‐to‐many distance CVs in PLUMED?

Thank you for any advice!