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

Diana Lousa dlousa at itqb.unl.pt
Wed Nov 19 16:32:48 CET 2008

On Wed, Nov 19, 2008 at 2:14 PM, Zhao Lifeng <zhao.lf at gmail.com> 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.


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
Oeiras, Portugal

> Lifeng Zhao
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081119/1cf94093/attachment.html>

More information about the gromacs.org_gmx-users mailing list