Dear users<div><br></div><div>I tried free energy calculation but grompp couldn't go through. It stops after</div><div><br></div><div>*******************</div><div><div>Generated 2278 of the 2278 non-bonded parameter combinations</div>
<div>Generating 1-4 interactions: fudge = 0.5</div><div>Generated 2278 of the 2278 1-4 parameter combinations</div><div>Excluding 3 bonded neighbours molecule type 'Protein'</div><div>turning H bonds into constraints...</div>
<div>Excluding 2 bonded neighbours molecule type 'SOL'</div><div>turning H bonds into constraints...</div><div>Excluding 1 bonded neighbours molecule type 'CL'</div><div>turning H bonds into constraints...</div>
<div>Coupling 1 copies of molecule type 'Protein'</div></div><div>*******************</div><div><br></div><div>The CPU usage is 100%. </div><div><br></div><div>I just add following into the mdp file:</div><div><div>
<br></div><div>***************</div><div>free_energy = yes </div><div>init_lambda = 0.0</div><div>delta_lambda = 0</div><div>sc_alpha =0.5</div><div>sc-power =1.0</div>
<div>sc-sigma = 0.3 </div><div>couple-moltype = Protein </div><div>couple-lambda0 = vdw-q</div><div>couple-lambda1 = none</div></div><div>***************</div><div><br></div>
<div>Does anyone have some idea about this problem? thanks.</div><div><br></div><div>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?</div>
<div><br></div><div>dawei</div><div><br></div><div><br></div><div><br></div>