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Residence time #43

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@BerndDoser BerndDoser commented Jul 11, 2024

Implement #42

@BerndDoser
add python code example
8ec98e6
@BerndDoser
Merge branch 'release-2024' into stop-criterion
0e40da6
@BerndDoser
Merge branch 'release-2024' into stop-criterion
86adec1
@BerndDoser
Add binding residues to RAMD group
3797eb1 
Refactor RAMD group initialization to use vector resizing
@BerndDoser
Add 4water RAMD tests for binding residues
3ae6555
@BerndDoser
read binding residues from mdp
2b672da
@BerndDoser
Change RAMD binding_residues from index to atom numbers
f1c0031
@BerndDoser
Test topology resinfo
62d9664
@BerndDoser
Update RAMD constructor to include mtop parameter
022ed97
@BerndDoser
add new pull group for testing
c339aad
@BerndDoser
calculate COM of extra groups
53a47f8
@BerndDoser
add extra groups only for RAMD
4f6e0e2
@BerndDoser
set pbcatom for extra groups
9bb5b0d
@BerndDoser
check COM distance against standard ramd group
46fa2d6 
set pull coord dim, vec, and eGeom
@BerndDoser
add residence_distance parameter and write residence time notice into…
2d3754c 
… log-file
@BerndDoser
Check if output file is defined for logging
d927062
@BerndDoser
change pull geometry from direction to distance for extra groups
83f21cf
@BerndDoser
write distances of extra groups to ramd output file
3362a67
@BerndDoser
separate function add_residence_time_groups
91f86a9
@BerndDoser
read binding index groups
d184a04
@BerndDoser
serialization of binding index groups
20cf0ce
@BerndDoser
build tpr file in unit test CalculateForces1WDHI
dd3451a
@BerndDoser
Check if binding group is defined
dd93ae3
@BerndDoser
read residence distance and
29cb3ef 
add mdp description to README
@BerndDoser
Add new mdp option ramd-residence-distance
af83d4b
@BerndDoser
Move 4water test data into own directory
0475e9b
@BerndDoser
add ramd-use-residence-dist as new mdp option
2837415
@BerndDoser
remove interaction group sulfur and
96d1654 
add backbone and carbon_not_backbone
@BerndDoser
add all residence interaction groups to pull groups
03339f1
@BerndDoser
fix launch 4water grompp ramd
9cfd553
BerndDoser added 20 commits March 5, 2024 11:06
@BerndDoser
define residence time interactions
1aebaaf
@BerndDoser
Instead of defining a pull coord with zero force constant, the flag n…
2146a0b 
…eedToCalcCom will be used
@BerndDoser
calculate COM only for non empty pull groups
377d39c
@BerndDoser
use default pbc atom for extra pull groups
f016e25
@BerndDoser
Merge branch 'release-2024' into stop-criterion
730ed54
@BerndDoser
Loop over residence interactions to calculate the COM distances
ce911b5
@BerndDoser
only calculate residence_contacts if use_residence_dist = true
966a989
@BerndDoser
add extra groups only if they are available in the index file
cc8797b
@BerndDoser
fix empty residence contacts
92b81bc
@BerndDoser
Comment out external data volume for debugging purposes
1d875bb
@BerndDoser
Replace explicit chemical binding groups
e627d94 
by general binding groups
@BerndDoser
remove chemical interaction pairs
22741f5
@BerndDoser
Revert "Update RAMD constructor to include mtop parameter"
84699d7 
This reverts commit 022ed97.
@BerndDoser
use extra pull groups pairwise as residence contacts
c267312
@BerndDoser
add 4water as RAMD_residence_time module test
aeafe22
@BerndDoser
fix extra pull groups for residence time
70e582e 
by calling process_pull_groups after add_residence_time_groups
@BerndDoser
add all extra residence time pull groups to inputrecStrings->pullGrou…
8f3f0b5 
…pNames for validation
@BerndDoser
test jenkins trigger
3b01cf0
@BerndDoser
fix wrong offset to extra residence time pull groups
91d3dff
@BerndDoser
Add residence_dist_reached, to print notification only once and to av…
83631f6 
…oid unneeded calculations
@BerndDoser BerndDoser self-assigned this Jul 11, 2024
@BerndDoser BerndDoser added this to the 2.2 milestone Jul 11, 2024
@BerndDoser BerndDoser linked an issue Jul 11, 2024 that may be closed by this pull request
Residence time #42
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Residence time

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