<div>Dear all users,</div>
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<div>1,</div>
<div>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].</div>
<div>Is it possible for me to provide only the parameters of B but le the grompp using the default parametes of initial structure A? </div>
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<div>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?</div>
<div>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. </div>
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<div>2,</div>
<div>When comparing the solvation free energy tutorial from <a href="http://md.chem.rug.nl/">http://md.chem.rug.nl</a> and the wiki(Dillgroup), I get confused at the definition of solvation free energy.</div>
<div>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.</div>
<div>Did I misunderstand anything here?</div>
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<div>thanks a lot</div>
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<div>LQin </div>
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