[gmx-users] distance restraints in mdp

[Sana Saeed]

i am performing protein ligand binding free energy calculation MD. i have applied distance restraint to 1 pair of atoms. now when i am running md it gives me LINCS warnings. first i thought it is because of wrong geometry so i changed complex, now i am doing it for Lysozyme+JZ4. but still same warning. i am confused about the distance restraints to be introduced in mdp file. disre = simple/ensemble? i read in manual, but still confused. i tried both with "simple it gives me LINCS warning and with ensemble it says that this version of gromacs doesnt support it. i am using 5.1 gromacs. Sana Saeed Khan,