<br><br><div class="gmail_quote">On Wed, Nov 19, 2008 at 2:14 PM, Zhao Lifeng <span dir="ltr"><<a href="mailto:zhao.lf@gmail.com">zhao.lf@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>Dear all,<br><br>I encountered a problem in alchemistry free energy calculations:<br><br>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).<br>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.<br>
And interactions between A and B were excluded in the simulations. However, the vibration mode would not be correct <br>for both A and B state.<br><br>Another scheme is to change the corresponding atoms to zero mass dummy atoms or from them. In this case, there will be<br>
no interactions on the dummy atoms, either bonded or non-bonded interactions. <br><br>I don't know if these schemes are correct and if there is any other more reasonable schemes. In my simulations I prefered the <br>
later one and thus the problems came. <br>
In state of lambda=0 or =1, since there are dummy atoms with no force on them, (sometimes with velocities, e.g. from <br>the
last lambda simulation), the dummy atoms often bring forth errors,
for example, 1-4 distance too large, neighbor list error<br>
and segmentation fault. Bond constraints seems work but it might not be reasonable for heavy atoms.<br><br>Any suggestions would be appreciated.</blockquote><div><br>Hello,<br><br>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.<br>
<br>Diana Lousa<br>PhD student<br>Protein Modelling Laboratory<br>ITQB/UNL <br>Oeiras, Portugal<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br><font color="#888888"><br><br><br><br>Lifeng Zhao
</font><br>_______________________________________________<br>
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