normal How could I solve constraint(?) problem

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3 years 3 weeks ago #8872 by Jinyoung
How could I solve constraint(?) problem was created by Jinyoung
Hi everyone,
I'v tried to practice simulation for transmembrane protein-POPC bilayer system
I downloaded the parameter files and structure files from CHARMM-GUI.
But as the system size is smaller than I expected, I removed the water solvent and re-solvate as below:

python insane.py -f nopbc_nosolv_system.gro -pbc square -box ${box_x},${box_y},75 -salt 0.15 -sol PW -o system_solv_ions.gro

And When I tried to run equilibration step after minimization step, I encountered the errors below:

ERROR: Cannot have constraint (1-2) with virtual site (2)
ERROR: Cannot have constraint (5-6) with virtual site (6)
ERROR: Cannot have constraint (34-35) with virtual site (35)
ERROR: Cannot have constraint (42-43) with virtual site (43)
ERROR: Cannot have constraint (61-62) with virtual site (62)
ERROR: Cannot have constraint (66-67) with virtual site (67)
ERROR: Cannot have constraint (74-75) with virtual site (75)
ERROR: Cannot have constraint (83-84) with virtual site (84)
ERROR: Cannot have constraint (87-88) with virtual site (88)
ERROR: Cannot have constraint (91-92) with virtual site (92)
ERROR: Cannot have constraint (97-98) with virtual site (98)

...

How can I solve this problem? I'm wondering Is there any what I' missing?
Thanks!

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3 years 3 weeks ago #8874 by vainikka
Replied by vainikka on topic How could I solve constraint(?) problem
Martini 2 POPC does not have any constraints nor virtual sites, so I'm wondering what it is that you are simulating. Does your protein contain constraints?

As for the error message: The problem is literally what's in the message. Your topology has constraints defined between virtual sites and regular beads/atoms/other virtual sites. This is a no-no.

Check out the grompp manual page: manual.gromacs.org/documentation/2021/on...help/gmx-grompp.html

"By default, all bonded interactions which have constant energy due to virtual site constructions will be removed. If this constant energy is not zero, this will result in a shift in the total energy. All bonded interactions can be kept by turning off -rmvsbds. Additionally, all constraints for distances which will be constant anyway because of virtual site constructions will be removed. If any constraints remain which involve virtual sites, a fatal error will result."

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