[gmx-users] Re: Internal water in the membrane receptor
jmsstarlight at gmail.com
Mon Feb 27 10:35:45 CET 2012
I've found a possible sollution to restrict oxygens of my X-ray water by
possible plasing the below string in the TOPOLOGY.top of my system
; Include X-ray water topology
; Include Position restraint file
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
I havent recieved any errors from gromp. Does this aproach correct in
I dont know why but after minimisation constrained mollecules were diffused
from the protein interious so POSRES have not worked :(
My minim.mdp consist of two separate posres for water as well as for ligand
groups ( there are no posre for protein).
define = -DPOSRES_LIG -DPOSRES_XW ; position restrain the protein
integrator = steep ; Algorithm (steep = steepest descent
emtol = 1000.0 ; Stop minimization when the maximum force <
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to
energygrps = Protein CAR
What should I add to that file to activate posres?
Finally are the constraints algorithm needed here ?
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