Namaste,
I have been trying to do a QM/MM-SMD with two variables in AMBER24
My cv.in file is like this:
cv_file
&colvar
cv_type = 'DISTANCE'
cv_ni = 2
cv_i = 4058,4063
npath = 2, path = 2.066, 5.28
path_mode = 'LINES'
nharm = 1, harm = 20
/
&colvar
cv_type = 'DISTANCE'
cv_ni = 2
cv_i = 4058,42691
npath = 2, path = 3.79, 2
path_mode = 'LINES'
nharm = 1, harm = 20
/
for that I got smd.txt file like this,
#
# MD time (ps), CV, handle_position, spring_constant, work
#
1005510.7500 2.06636522 4.12615628 2.06600000
3.79000000 20.00000000 20.00000000 0.00000000
1005510.7513 2.05846646 4.15303818 2.06921400
3.78821000 20.00000000 20.00000000 0.01290679
1005510.7525 2.05024689 4.17019098 2.07242800
3.78642000 20.00000000 20.00000000 0.02739091
1005510.7538 2.04184586 4.17894473 2.07564200
3.78463000 20.00000000 20.00000000 0.04313753
1005510.7550 2.03343208 4.18203172 2.07885600
3.78284000 20.00000000 20.00000000 0.05990040
1005510.7563 2.02529201 4.18129573 2.08207000
3.78105000 20.00000000 20.00000000 0.07750805
1005510.7575 2.01784775 4.17621789 2.08528400
3.77926000 20.00000000 20.00000000 0.09578984
...............................................................................................................................................................................................................
...............................................................................................................................................................................................................
1005511.9850 4.38798259 2.58472818 5.24143200
2.02148000 20.00000000 20.00000000 56.34487880
1005511.9863 4.39500434 2.60615626 5.24464600
2.01969000 20.00000000 20.00000000 56.42016858
1005511.9875 4.40242898 2.63352742 5.24786000
2.01790000 20.00000000 20.00000000 56.49616725
1005511.9888 4.41023979 2.65406899 5.25107400
2.01611000 20.00000000 20.00000000 56.57284339
1005511.9900 4.41842767 2.65692696 5.25428800
2.01432000 20.00000000 20.00000000 56.64971617
1005511.9913 4.42692184 2.63889218 5.25750200
2.01253000 20.00000000 20.00000000 56.72604776
1005511.9925 4.43558952 2.60517307 5.26071600
2.01074000 20.00000000 20.00000000 56.80114545
1005511.9938 4.44437174 2.56816101 5.26393000
2.00895000 20.00000000 20.00000000 56.87464388
1005511.9950 4.45319936 2.54191429 5.26714400
2.00716000 20.00000000 20.00000000 56.94668102
1005511.9963 4.46201203 2.53173721 5.27035800
2.00537000 20.00000000 20.00000000 57.01777547
1005511.9975 4.47073990 2.52991557 5.27357200
2.00358000 20.00000000 20.00000000 57.08839451
1005511.9988 4.47935255 2.52525771 5.27678600
2.00179000 20.00000000 20.00000000 57.15864012
#
# <> total work done: 57.2144092001
Here, I am unable to understand how to reweight the trajectory according to
the Amber tutorial using WHAM or any other method to look at the energy
profile.
Need your suggestions
Thanks
--
Kriti Shukla
Research Scholar
Department of Chemistry
Indian Institute of Technology, Kharagpur
India. 721302
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Received on Fri Jun 06 2025 - 22:30:03 PDT
