Hi Erik,<br>I think also I can try proton-proton transfer with gromacs later when it will be implemented.<br><br>best,<br>Olga<br><br><div class="gmail_quote">2010/12/2 Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Olga Ivchenko skrev 2010-12-02 13.30:<div><div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear gromacs users,<br>
<br>
I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs.<br>
I read about umbrella sampling, but may be there is other techniques?<br>
<br>
Yours sincerely,<br>
Olga<br>
</blockquote></div></div>
I am working on a protocol to include proton transfer in classical gromacs simulations. Unfortunately it will note be ready for at least a month, so if you're in a hurry you'll have to do it with e.g. QM/MM.<br>
<br>
Erik<br>
<br>
-- <br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br>
<a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a><br><font color="#888888">
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