I have protein-ligand system. I have basic idea for energy minimization.mdp parameter.
;
integrator = steep
emtol = 10.0
emstep = 0.01
nsteps = 500
energygrps = Protein OAI
;
nstlist = 1
cutoff-scheme = Verlet
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
but I have not idea how to write the parameter where all the backbone heavy atoms of the protein have to be constrained with an elastic constant of 50 kcal /mol Å -2 and the other atoms should be free.
I never did these things, but something I can suggest you, try to make itp file for backbone heavy atoms to constrained with 50 kcal /mol Å -2 and export it via topology file.
Rehards,
Nandan
Generate a restraint file using 'gmx genrestr' Here is the link:
http://manual.gromacs.org/programs/gmx-genrestr.html
This will give you force constant values for all heavy atoms, set them all to your desired value.
Then you have to include this file in your topology in a way similar to this:
#ifdef POSRES
#include ""
#endif
In your mdp file you have to put a variable name 'Define'
Here you can read about this variable in the 'Preprocessing' section:
http://manual.gromacs.org/online/mdp_opt.html#pp
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