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Bug #2600

coul-lambdas turns off all coulombic interactions in system instead of the molecule specificed in the couple-moltype

Added by zhiyi wu 3 months ago.

Status:
New
Priority:
High
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

I have a ligand with zero partial charges and I'm interested in calculating the free energy of decoupling this ligand.
I have used couple-moltype to specify the molecule to be decoupled to ZR, which is the ligand.
Since the ligand ZR has no partial charge, I would expect coul-lambdas to do nothing.
However, setting the coul-lambdas to 1 turns off all coulombic interactions in the system, leading to water mixing with the membrane.
Setting coul-lambdas to 0, on the alther hand, keep the coulombic interactions on normally.

I have uploaded a short simulation as well as the file need to produce the tpr file (npt.tpr).
The tpr file can be generated by gmx grompp -f npt.mdp -c nvt.gro -o npt.tpr -n index.ndx
The genrated file is the npt.xtc

bug.tgz (12.2 MB) bug.tgz zhiyi wu, 08/07/2018 06:50 PM

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