[gmx-users] DUMMY and CONSTRAINED

[acorrea at unisa.it]

Hallo.
I would like to performe a all-bonds constrain molecular dynamics, (I think with
 shake) but I have dummy atoms in my sistems and I must define bonds respect
these dummy atoms. 
If I put in a file.mdp :

constrained = all-bonds
constraint-algorithm     = Shake


in the compilation step I found (atoms 27 and 28 are two dummy atoms):


double-checking input for internal consistency...
Cleaning up constraints and constant bonded interactions with dummy particles
ERROR: Cannot have constraint (1-27) with dummy atom (27)
ERROR: Cannot have constraint (11-28) with dummy atom (28)
ERROR: Cannot have constraint (10-28) with dummy atom (28)
ERROR: Cannot have constraint (9-28) with dummy atom (28)
ERROR: Cannot have constraint (8-28) with dummy atom (28)
ERROR: Cannot have constraint (7-28) with dummy atom (28)
ERROR: Cannot have constraint (6-27) with dummy atom (27)
ERROR: Cannot have constraint (5-27) with dummy atom (27)
ERROR: Cannot have constraint (4-27) with dummy atom (27)
ERROR: Cannot have constraint (3-27) with dummy atom (27)
ERROR: Cannot have constraint (2-27) with dummy atom (27)
ERROR: Cannot have constraint (1-28) with dummy atom (28)
Fatal error: There were 12 dummy atoms involved in constraints


But I need to put shake also on this bonds 

What can I performe all-bonds constrain dynamic?

Thank you. 




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