On Wed, Nov 19, 2008 at 2:14 PM, Zhao Lifeng <[EMAIL PROTECTED]> wrote:
> > 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. Hello, I have used schemes similar to the one you described and to circumvent the problems associated with growing or disappearing particles out of nothing I used soft-core interactions and manipulated the soft-core parameters to get "nice" dgdl curves. Hope this helps. Diana Lousa PhD student Protein Modelling Laboratory ITQB/UNL Oeiras, Portugal > > > > > > Lifeng Zhao > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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