[gmx-users] Constraints specified in .mdp as well as in .top files

[Vishwanath Dalvi]

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?

Thanks!

Ashwin



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