Vishwanath Dalvi wrote:
Hi!
I have a question about a possible redundancy/conflict in specifying
bond-constraints.
I have in my simulation (among other things) a number of bonds - some of
which are harmonic while some are rigid (or constrained).
I specify the bonds in the .itp (or ultimately in the .top) files as
follows:
[ bonds ]
; index1 index2 func deq(nm) k(kJ/mol/nm2)
1 2 1 0.1529000000 224262.4000000000
1 32 1 0.1810000000 185769.6000000000
2 3 1 0.1529000000 224262.4000000000
3 4 1 0.1529000000 224262.4000000000
[ constraints ]
; index1 index2 funct length(nm)
1 30 1 0.1090000000
1 31 1 0.1090000000
2 28 1 0.1090000000
2 29 1 0.1090000000
However, it turns out that the .mdp file also requires one to specify
constraints in the form of:
constraints = all-bonds/h-bonds etc
Do we have to specify constraints in the .mdp file if we already have
specified them in the .itp file?
I believe so. This is also true of restraints (which are a different
concept in GROMACS).
Mark
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