Dear users, I used acpype to get a topology for ADP.While minimizing energy one hydrogen moves too much to an oxygen, ending with the oxygen "swallowing" the hydrogen totally. They got exact the same coordinates in the .gro output. In the topology the parameters for that H (h0) are missing: [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb... h1 h1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 h2 h2 0.00000 0.00000 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157... I found parameters (ho ho 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.00 0.0000) in the wiki (last question):https://code.google.com/archive/p/acpype/wikis/FAQ.wiki Can someone confirm these parameters since there is no source. Best regards,olaf
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