GROMACS version:2023.3
GROMACS modification: Yes/No
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Hello All
I am trying to pull two large CG vesicles that are aligned along the X axis from 51 nm distance to 1 nm. Below is the MDP options I used, which worked for another system.
; COM PULLING
pull = yes
; Cylinder radius for dynamic reaction force groups (nm)
pull-cylinder-r = 1.5
pull-constr-tol = 1e-06
pull-print-com = yes
pull-print-ref-value = no
pull-print-components = no
pull-nstxout = 50
pull-nstfout = 50
pull-pbc-ref-prev-step-com = yes
pull-xout-average = no
pull-fout-average = no
; Number of pull groups
pull-ngroups = 2
; Number of pull coordinates
pull-ncoords = 1
; Group and coordinate parameters
pull-group1-name = ves1 ;lipids and water and ions inside of the left vesicle
pull-group2-name = ves2 ; lipids and water and ions inside of the right vesicle
pull-group1-weights =
pull-group1-pbcatom = 542874
pull-group2-pbcatom = 1920406
pull-coord1-type = constant-force
pull-coord1-potential-provider =
pull-coord1-expression =
pull-coord1-dx = 1e-09
pull-coord1-geometry = distance
pull-coord1-groups = 1 2
pull-coord1-dim = Y N N
pull-coord1-start = yes
pull-coord1-init =
pull-coord1-rate = 0.001 ; 0.001nm per ps = 1 nm per 1 ns
pull-coord1-k = 1000 ; KJ mol-1 nm -1
pull-coord1-kB = 0
This set up worked for a similar system but it fails for the current one with this following error message.
Note that mdrun will redetermine rlist based on the actual pair-list setup
Pull group natoms pbc atom distance at start reference at t=0
1 340857 542874
2 343395 1920406
Program: gmx grompp, version 2023.3
Source file: src/gromacs/pulling/pull.cpp (line 525)
Fatal error:
Distance between pull groups 1 and 2 (51.721501 nm) is larger than 0.49 times
the box size (50.828498).
The box sizes are 103.73163 51.86582 51.86582, and hence the X axis is clearly longer than the starting COM distance.
Could you tell me how to change the parameters to resolve the error?
Thanks in advance
Sunjoo