Dear all users, 1, I am modifying the .top file for mutation free energy calculation(A->B), so I need the provide the parameters of structure A and B in [bonds], [angles], [dihedrals]. Is it possible for me to provide only the parameters of B but le the grompp using the default parametes of initial structure A?
I know the A parameters will be copied to B if parameters of B is not explicitly defined in .top. IS that means I must explicitly define both A and B at the same time? I ask it since I find in OPLSAA force field the .top file does not contain paramters of [bonds], [angles],... but only the atome numbers and function types. 2, When comparing the solvation free energy tutorial from http://md.chem.rug.nl and the wiki(Dillgroup), I get confused at the definition of solvation free energy. In the former, dG=dG1(in vacuo)-dG2(in water); however, in the latter it seems only calculating the dG2(in water) gives excellent result compared to expt. Did I misunderstand anything here? thanks a lot LQin
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