Remove L-W ixn group and merge w/P-L group

jkausrelay commented 2 weeks ago

Remove the L-W specific ixn group and merge it back in with the P-L (now env-L) ixn gorup.
This should improve performance
Maintain backward compatibility with FFs that have a separate 'solvent' section if the parameters match those of the original ixn group

badisa commented 1 week ago

Could you post the benchmarks for timemachine before and after this change?

jkausrelay commented 1 week ago

Could you post the benchmarks for timemachine before and after this change?

Before

dhfr-apo: N=23558 speed: 404.43ns/day dt: 2.5fs (ran 100000 steps in 53.41s)
dhfr-apo-barostat-interval-25: N=23558 speed: 336.40ns/day dt: 2.5fs (ran 100000 steps in 64.21s)
building a protein system with 1758 protein atoms and 7047 water atoms
Optimizing initial state at λ=0.1
----------------------------------------------------------------------
performing BFGS minimization on 265 atoms
(holding the other 8575 atoms frozen)
U(x_0) = -102393.346
Warning: Desired error not necessarily achieved due to precision loss.
         Current function value: -103237.889515
         Iterations: 361
         Function evaluations: 511
         Gradient evaluations: 495
U(x_final) = -103237.890
atom with highest force norm after minimization: 1117
force(x_final)[1117] = [-261.1905371    99.43120306  171.57122914]
----------------------------------------------------------------------
hif2a-apo: N=8805 speed: 731.04ns/day dt: 2.5fs (ran 100000 steps in 29.55s)
hif2a-apo-barostat-interval-25: N=8805 speed: 557.70ns/day dt: 2.5fs (ran 100000 steps in 38.73s)
hif2a-rbfe-barostat-interval-25: N=8840 speed: 521.50ns/day dt: 2.5fs (ran 100000 steps in 41.42s)
hif2a-rbfe-local: N=8840 speed: 1390.43ns/day dt: 2.5fs (ran 100000 steps in 15.54s)
hif2a-rbfe-barostat-interval-25-water-sampling-interval-400: N=8840 speed: 492.19ns/day dt: 2.5fs (ran 100000 steps in 43.89s)
Optimizing initial state at λ=0.1
----------------------------------------------------------------------
performing BFGS minimization on 199 atoms
(holding the other 6118 atoms frozen)
U(x_0) = -83324.835
Warning: Desired error not necessarily achieved due to precision loss.
         Current function value: -84115.276026
         Iterations: 435
         Function evaluations: 552
         Gradient evaluations: 541
U(x_final) = -84115.276
atom with highest force norm after minimization: 645
force(x_final)[645] = [ 232.67846235  -71.46603238 -425.10828159]
----------------------------------------------------------------------
solvent-apo: N=6282 speed: 1129.21ns/day dt: 2.5fs (ran 100000 steps in 19.13s)
solvent-apo-barostat-interval-25: N=6282 speed: 805.42ns/day dt: 2.5fs (ran 100000 steps in 26.82s)
solvent-rbfe-barostat-interval-25: N=6317 speed: 699.10ns/day dt: 2.5fs (ran 100000 steps in 30.90s)
solvent-rbfe-local: N=6317 speed: 1514.54ns/day dt: 2.5fs (ran 100000 steps in 14.27s)

After

dhfr-apo: N=23558 speed: 416.20ns/day dt: 2.5fs (ran 100000 steps in 51.90s)
dhfr-apo-barostat-interval-25: N=23558 speed: 361.76ns/day dt: 2.5fs (ran 100000 steps in 59.71s)
building a protein system with 1758 protein atoms and 7047 water atoms
Optimizing initial state at λ=0.1
----------------------------------------------------------------------
performing BFGS minimization on 265 atoms
(holding the other 8575 atoms frozen)
U(x_0) = -102393.346
Warning: Desired error not necessarily achieved due to precision loss.
         Current function value: -103237.889515
         Iterations: 361
         Function evaluations: 511
         Gradient evaluations: 495
U(x_final) = -103237.890
atom with highest force norm after minimization: 1117
force(x_final)[1117] = [-261.1905371    99.43120306  171.57122914]
----------------------------------------------------------------------
hif2a-apo: N=8805 speed: 739.97ns/day dt: 2.5fs (ran 100000 steps in 29.19s)
hif2a-apo-barostat-interval-25: N=8805 speed: 590.91ns/day dt: 2.5fs (ran 100000 steps in 36.56s)
hif2a-rbfe-barostat-interval-25: N=8840 speed: 534.30ns/day dt: 2.5fs (ran 100000 steps in 40.43s)
hif2a-rbfe-local: N=8840 speed: 1394.69ns/day dt: 2.5fs (ran 100000 steps in 15.49s)
hif2a-rbfe-barostat-interval-25-water-sampling-interval-400: N=8840 speed: 502.39ns/day dt: 2.5fs (ran 100000 steps in 43.00s)
Optimizing initial state at λ=0.1
----------------------------------------------------------------------
performing BFGS minimization on 199 atoms
(holding the other 6118 atoms frozen)
U(x_0) = -83324.835
Warning: Desired error not necessarily achieved due to precision loss.
         Current function value: -84115.276026
         Iterations: 435
         Function evaluations: 552
         Gradient evaluations: 541
U(x_final) = -84115.276
atom with highest force norm after minimization: 645
force(x_final)[645] = [ 232.67846235  -71.46603238 -425.10828159]
----------------------------------------------------------------------
solvent-apo: N=6282 speed: 1127.16ns/day dt: 2.5fs (ran 100000 steps in 19.17s)
solvent-apo-barostat-interval-25: N=6282 speed: 821.17ns/day dt: 2.5fs (ran 100000 steps in 26.31s)
solvent-rbfe-barostat-interval-25: N=6317 speed: 701.33ns/day dt: 2.5fs (ran 100000 steps in 30.80s)
solvent-rbfe-local: N=6317 speed: 1521.32ns/day dt: 2.5fs (ran 100000 steps in 14.20s)

proteneer / timemachine

Remove L-W ixn group and merge w/P-L group #1372