[gmx-users] Alchemistry free energy simulations of molecules with different atom numbers

Zhao Lifeng zhao.lf at gmail.com
Wed Nov 19 15:14:20 CET 2008

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

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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