Dear users I tried free energy calculation but grompp couldn't go through. It stops after
******************* Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning H bonds into constraints... Coupling 1 copies of molecule type 'Protein' ******************* The CPU usage is 100%. I just add following into the mdp file: *************** free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 couple-moltype = Protein couple-lambda0 = vdw-q couple-lambda1 = none *************** Does anyone have some idea about this problem? thanks. Another question is whether I can switch off "two molecules" (such as protein+ligand) in free energy calculation? I searched this list and got that 4.0.7 did support this. how about 4.5.4? dawei
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