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[WIP] Alchemical Custom Forces + Custom Lennard-Jones Switching #431

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[WIP] Alchemical Custom Forces + Custom Lennard-Jones Switching #431

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76bde74
Added custom Lennard-Jones switching functions
Olllom Feb 6, 2019
883c193
Clean up implementation and documentation of forcefactories
Olllom Feb 6, 2019
44dc396
Added a testsystem for solvation using charmm input files
Olllom Jul 17, 2019
51ea8fe
CharmmSolvated testsystem optionally without vdw/charges
Olllom Jul 18, 2019
259caf5
alchemical softcore for custom forces
Olllom Jul 18, 2019
30e1ecb
bugfix in charmm testsystem and vdw factory
Olllom Jul 20, 2019
b6aecf8
Modifying custom forces.
Olllom Jul 20, 2019
606c339
Merge branch 'master' into vdw_switching
Olllom Jul 20, 2019
c3af895
Merge branch 'master' of github.com:choderalab/openmmtools into vdw_s…
Olllom Sep 23, 2019
a163240
merge master into vdw_switching
Olllom Oct 21, 2019
bbe0e74
added energy comparison to charmm for lj switch
Olllom Dec 7, 2019
7d77d72
bugfix
Olllom Dec 7, 2019
6cc4192
CHARMM reference for uncharged and annihilated energies
Olllom Dec 7, 2019
b9ec52e
rename get_energy to calculate_energy in LJPairBox
Olllom Dec 7, 2019
af68f39
Merge branch 'master' into vdw_switching
Olllom Dec 7, 2019
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409 changes: 407 additions & 2 deletions openmmtools/alchemy.py
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196 changes: 196 additions & 0 deletions openmmtools/data/charmm-solvated/envi.str
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Original file line number Diff line number Diff line change
@@ -0,0 +1,196 @@
* STREAM FILE FOR ENVIRONMENT
*

set nat ?NATC
set app
!We're exploiting what is arguably a bug in the parser. On the left hand side,
!the quotes have priority, so NAT is correctly substituted. On the right hand
!side, the ? has priority and NATC" (sic) is not a valid substitution...
if "@NAT" ne "?NATC" if @nat ne 0 set app append


READ RTF CARD @{app}
* Constructed Based on Stream File from CGenff
*
36 1

MASS -1 CCX2 12.01100 C
MASS -1 HCX2 1.00800 H
MASS -1 OCX1 15.99940 O
MASS -1 HOX1 1.00800 H
MASS -1 CCX3 12.01100 C
MASS -1 HCX3 1.00800 H
MASS -1 HT 1.00800 H
MASS -1 OT 15.99940 O
MASS -1 CLA 35.45000 CL
MASS -1 POT 39.09830 K

DEFA FIRS NONE LAST NONE
AUTO ANGLES DIHE DRUDE

RESI OCOH 0.000 ! PARAM_PENALTY=0.0000 ; CHARGE_PENALTY=0.0000
GROUP ! CHARGE CH_PENALTY
ATOM C1 CCX2 0.050 ! 0.000
ATOM H11 HCX2 0.090 ! 0.000
ATOM H12 HCX2 0.090 ! 0.000
ATOM O1 OCX1 -0.649 ! 0.000
ATOM HO1 HOX1 0.420 ! 0.000
ATOM C2 CCX2 -0.181 ! 0.000
ATOM H21 HCX2 0.090 ! 0.000
ATOM H22 HCX2 0.090 ! 0.000
ATOM C3 CCX2 -0.180 ! 0.000
ATOM H31 HCX2 0.090 ! 0.000
ATOM H32 HCX2 0.090 ! 0.000
ATOM C4 CCX2 -0.180 ! 0.000
ATOM H41 HCX2 0.090 ! 0.000
ATOM H42 HCX2 0.090 ! 0.000
ATOM C5 CCX2 -0.180 ! 0.000
ATOM H51 HCX2 0.090 ! 0.000
ATOM H52 HCX2 0.090 ! 0.000
ATOM C6 CCX2 -0.180 ! 0.000
ATOM H61 HCX2 0.090 ! 0.000
ATOM H62 HCX2 0.090 ! 0.000
ATOM C7 CCX2 -0.180 ! 0.000
ATOM H71 HCX2 0.090 ! 0.000
ATOM H72 HCX2 0.090 ! 0.000
ATOM C8 CCX3 -0.270 ! 0.000
ATOM H81 HCX3 0.090 ! 0.000
ATOM H82 HCX3 0.090 ! 0.000
ATOM H83 HCX3 0.090 ! 0.000

BOND H12 C1
BOND H31 C3
BOND H51 C5
BOND H71 C7
BOND H42 C4
BOND H22 C2
BOND H62 C6
BOND H82 C8
BOND C1 H11
BOND C1 C2
BOND C1 O1
BOND C3 C2
BOND C3 C4
BOND C3 H32
BOND C5 C4
BOND C5 C6
BOND C5 H52
BOND C7 C6
BOND C7 C8
BOND C7 H72
BOND H83 C8
BOND C2 H21
BOND C4 H41
BOND C6 H61
BOND C8 H81
BOND HO1 O1

RESI TIP3 0.000
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
ANGLE H1 OH2 H2 ! required
DONOR H1 OH2
DONOR H2 OH2
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE

RESI POT 1.00 ! Potassium Ion
GROUP
ATOM POT POT 1.00
PATCHING FIRST NONE LAST NONE

RESI CLA -1.00 ! Chloride Ion
GROUP
ATOM CLA CLA -1.00
PATCHING FIRST NONE LAST NONE

END

READ PARA CARD FLEX @{APP}
* PARAMETERS FOR ENVIR
*


ATOMS
MASS -1 CCX2 12.01100 ! CGENFF_PRM
MASS -1 HCX2 1.00800 ! CGENFF_PRM
MASS -1 OCX1 15.99940 ! CGENFF_PRM
MASS -1 HOX1 1.00800 ! CGENFF_PRM
MASS -1 CCX3 12.01100 ! CGENFF_PRM
MASS -1 HCX3 1.00800 ! CGENFF_PRM
MASS -1 HT 1.00800 ! CGENFF_PRM
MASS -1 OT 15.99940 ! CGENFF_PRM
MASS -1 CLA 35.45000 ! CGENFF_PRM
MASS -1 POT 39.09830 ! CGENFF_PRM


BONDS
CCX2 CCX2 222.500 1.5300 ! CGENFF_PRM
CCX2 CCX3 222.500 1.5280 ! CGENFF_PRM
CCX2 OCX1 428.000 1.4200 ! CGENFF_PRM
CCX2 HCX2 309.000 1.1110 ! CGENFF_PRM
CCX3 HCX3 322.000 1.1110 ! CGENFF_PRM
OCX1 HOX1 545.000 0.9600 ! CGENFF_PRM
HT HT 0.0 1.5139 ! CGENFF_PRM
HT OT 450.000 0.9572 ! CGENFF_PRM

ANGLES
CCX2 CCX2 CCX2 58.350 113.6000 11.160 2.5610 ! CGENFF_PRM
CCX2 CCX2 CCX3 58.000 115.0000 8.000 2.5610 ! CGENFF_PRM
CCX2 CCX2 OCX1 75.700 110.1000 ! CGENFF_PRM
CCX2 CCX2 HCX2 26.500 110.1000 22.530 2.1790 ! CGENFF_PRM
CCX3 CCX2 HCX2 34.600 110.1000 22.530 2.1790 ! CGENFF_PRM
OCX1 CCX2 HCX2 45.900 108.8900 ! CGENFF_PRM
HCX2 CCX2 HCX2 35.500 109.0000 5.400 1.8020 ! CGENFF_PRM
CCX2 CCX3 HCX3 34.600 110.1000 22.530 2.1790 ! CGENFF_PRM
HCX3 CCX3 HCX3 35.500 108.4000 5.400 1.8020 ! CGENFF_PRM
CCX2 OCX1 HOX1 50.000 106.0000 ! CGENFF_PRM
HT OT HT 55.000 104.5200 ! CGENFF_PRM

DIHEDRALS
CCX2 CCX2 CCX2 CCX2 0.0645 2 0.00 ! CGENFF_PRM
CCX2 CCX2 CCX2 CCX2 0.1497 3 180.00 ! CGENFF_PRM
CCX2 CCX2 CCX2 CCX2 0.0946 4 0.00 ! CGENFF_PRM
CCX2 CCX2 CCX2 CCX2 0.1125 5 0.00 ! CGENFF_PRM
CCX2 CCX2 CCX2 CCX3 0.1505 2 0.00 ! CGENFF_PRM
CCX2 CCX2 CCX2 CCX3 0.0813 3 180.00 ! CGENFF_PRM
CCX2 CCX2 CCX2 CCX3 0.1082 4 0.00 ! CGENFF_PRM
CCX2 CCX2 CCX2 CCX3 0.2039 5 0.00 ! CGENFF_PRM
CCX2 CCX2 CCX2 OCX1 0.1950 3 0.00 ! CGENFF_PRM
CCX2 CCX2 CCX2 HCX2 0.1950 3 0.00 ! CGENFF_PRM
CCX3 CCX2 CCX2 HCX2 0.1800 3 0.00 ! CGENFF_PRM
OCX1 CCX2 CCX2 HCX2 0.1950 3 0.00 ! CGENFF_PRM
HCX2 CCX2 CCX2 HCX2 0.2200 3 0.00 ! CGENFF_PRM
CCX2 CCX2 CCX3 HCX3 0.1600 3 0.00 ! CGENFF_PRM
HCX2 CCX2 CCX3 HCX3 0.1600 3 0.00 ! CGENFF_PRM
CCX2 CCX2 OCX1 HOX1 1.1300 1 0.00 ! CGENFF_PRM
CCX2 CCX2 OCX1 HOX1 0.1400 2 0.00 ! CGENFF_PRM
CCX2 CCX2 OCX1 HOX1 0.2400 3 0.00 ! CGENFF_PRM
HCX2 CCX2 OCX1 HOX1 0.1800 3 0.00 ! CGENFF_PRM

IMPROPERS

NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
CCX2 0.0 -0.0560 2.0100 0.0 -0.0100 1.9000 ! CGENFF_PRM
HCX2 0.0 -0.0350 1.3400 ! CGENFF_PRM
OCX1 0.0 -0.1921 1.7650 ! CGENFF_PRM
HOX1 0.0 -0.0460 0.2245 ! CGENFF_PRM
CCX3 0.0 -0.0780 2.0500 0.0 -0.0100 1.9000 ! CGENFF_PRM
HCX3 0.0 -0.0240 1.3400 ! CGENFF_PRM
HT 0.0 -0.0460 0.2245 ! CGENFF_PRM
OT 0.0 -0.1521 1.7682 ! CGENFF_PRM
POT 0.0 -0.0870 1.76375 ! CGENFF_PRM
CLA 0.0 -0.1500 2.27 ! CGENFF_PRM


NBFIX
POT CLA -0.114236 4.081 ! CGENFF_PRM

HBOND CUTHB 0.5

END

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