Dear all, I encountered a problem in alchemistry free energy calculations:
In my simulations a group (A) is to be changed to (B) in a molecule, while the atom numbers n(A) is not equal to n(B). A scheme is to include both A and B in the same topology file and switch on/off the B/A charges and vdw interactions. And interactions between A and B were excluded in the simulations. However, the vibration mode would not be correct for both A and B state. Another scheme is to change the corresponding atoms to zero mass dummy atoms or from them. In this case, there will be no interactions on the dummy atoms, either bonded or non-bonded interactions. I don't know if these schemes are correct and if there is any other more reasonable schemes. In my simulations I prefered the later one and thus the problems came. In state of lambda=0 or =1, since there are dummy atoms with no force on them, (sometimes with velocities, e.g. from the last lambda simulation), the dummy atoms often bring forth errors, for example, 1-4 distance too large, neighbor list error and segmentation fault. Bond constraints seems work but it might not be reasonable for heavy atoms. Any suggestions would be appreciated. Lifeng Zhao
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