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I’m trying to carry out umbrella sampling where my collective variable is distance between ATP and residues that are within 5 Angstrom distance of the ATP. The simulation runs for few ps and then gives the error:
step 572320: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Can anyone help me with this problem ?
My pull code looks like the following:
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = r_3_4_308_309_310_311_339_340_342_343_345
pull_group2_name = ATP_ATP_401
pull-group1-pbcatom = 1191
pull-pbc-ref-prev-step-com = yes
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = Y N N ; pull along Z
pull_coord1_groups = 1 2 ; groups 1 (Chain A) and 2 (Chain B) define the reaction coordinate
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.02 ; 0.01 nm per ps
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
Does it help if you pull slower? Try pull_coord1_rate = 0.002.