[gmx-users] protein constrained, ligand ot constrained

mollica.luca at hsr.it mollica.luca at hsr.it
Sun Apr 15 12:06:20 CEST 2007

Dear all,
I would like to set up a simulation of a protein-ligand system with the
protein left bond-constrained using LINCS algorithm and the ligand left
unconstrained, i.e. in order to check the effect of some variations of
force constants that I have computed on the protein-ligand interactions.
Do you have any suggestion about this issue ?
Actually, the only solution that I have (as suggested by someone else,
also) is to use the mdp option

constraints    =   none

and write a new section for the protein topology of this kind (values
are w/o meaning):


1 2 1 0.150
1 3 1 0.179
2 9 1 0.130

etc etc ... an almost simple script could do the job.
This method seems to me, by now, the right one, but do you know any
other more straightforward method for performing this operation ?

Thanx in advance


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