Dear all,When I performing mutation free energy calculation from Leu to Ala, I first turn off the charge on the side chain of Leu. As I read from the GMX archive, the dG/dl curve should be rather smooth for turning off the partial charge. In this step(charge off/on), however, I can not obtain the expected smooth dGdl curve.(see the attachment). I did not use soft-core in this step. Is this normal because the mutation is relatively large? If not, what could be the problem?
the following is part of the topology file.17 opls_238 2 LEU N 7 -0.5 14.0067 ; qtot 0.5 18 opls_241 2 LEU H 7 0.3 1.008 ; qtot 0.8 19 opls_224B 2 LEU CA 7 0.14 12.011 ; qtot 0.94 20 opls_140 2 LEU HA 7 0.06 1.008 ; qtot 1 21 opls_136 2 LEU CB 8 -0.12 12.011 opls_136 0 12.011 ; qtot 0.88 22 opls_140 2 LEU HB1 8 0.06 1.008 opls_140 0 1.008 ; qtot 0.94 23 opls_140 2 LEU HB2 8 0.06 1.008 opls_140 0 1.008 ; qtot 1 24 opls_137 2 LEU CG 9 -0.06 12.011 opls_137 0 12.011 ; qtot 0.94 25 opls_140 2 LEU HG 9 0.06 1.008 opls_140 0 1.008 ; qtot 1 26 opls_135 2 LEU CD1 10 -0.18 12.011 opls_135 0 12.011 ; qtot 0.82 27 opls_140 2 LEU HD11 10 0.06 1.008 opls_140 0 1.008 ; qtot 0.88 28 opls_140 2 LEU HD12 10 0.06 1.008 opls_140 0 1.008 ; qtot 0.94 29 opls_140 2 LEU HD13 10 0.06 1.008 opls_140 0 1.008 ; qtot 1 30 opls_135 2 LEU CD2 11 -0.18 12.011 opls_135 0 12.011 ; qtot 0.82 31 opls_140 2 LEU HD21 11 0.06 1.008 opls_140 0 1.008 ; qtot 0.88 32 opls_140 2 LEU HD22 11 0.06 1.008 opls_140 0 1.008 ; qtot 0.94 33 opls_140 2 LEU HD23 11 0.06 1.008 opls_140 0 1.008 ; qtot 1 34 opls_235 2 LEU C 12 0.5 12.011 ; qtot 1.5 35 opls_236 2 LEU O 12 -0.5 15.9994 ; qtot 1
thank you Qiang
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