[gmx-users] problem using grompp

[Sotirios Dionysios I. Papadatos]

Dear community,


I am trying to set parameters for a molecule that doesn't exist in gromacs "library".

I have found all the required data from the literature, apart from bond force constant (Kb).

There seems to be a way to overcome this but using constraints on all the bonds using the Settle algorithm. My problem is that even by looking through the manual I haven't found a way to implement it. I believe I do know that it has to be used in the .mdp file but I don't know how.

So far I have tried adding these two lines in the .mdp file:

constraints=all-bonds

constraint-algorithm=settle

But it doesn't seem to do the trick, it still prints out the same error!