<html><head><meta http-equiv=Content-Type content="text/html; charset=iso-8859-1"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Tahoma, sans-serif; font-size: 13px; '>The standard procedure of H+ interchange and transition states can be done <br>through QM/MM.<br>Please give one reference according to the algorithms you have mentioned.<br><br>Cheers.<br><br>>>> Joćo M. Damas<jmdamas@itqb.unl.pt> 06.09.11 15.19 Uhr >>><br>
As Justin said, constant protonation != constant pH.<div><br></div><div>Constant-pH MD does not simulate H+, but allows changes in protonation states during the MD simulation. There are different algorithms to accomplish that.</div>
<div><br></div><div>Cheers,</div><div>Joćo<br><br><div class="gmail_quote">On Tue, Sep 6, 2011 at 2:04 PM, Emanuel Peter <span dir="ltr"><<a href="mailto:Emanuel.Peter@chemie.uni-regensburg.de">Emanuel.Peter@chemie.uni-regensburg.de</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;"><div style="font-family: Tahoma,sans-serif; font-size: 13px;">Could you just tell me smth. !<br>No forcefield on whole earth is able to reproduce the pH realistically<br>
by H+.<br>You just can apply pH of your system through the protonation states<br>of each part in your system.<br><br>monkey.<br><br><br><br>>>> Joćo M. Damas<u></u> 06.09.11 14.22 Uhr >>><div><div></div>
<div class="h5"><br>
That is not considered constant-pH MD.<div><br></div><div>Follow Justin's suggestion.</div><div><br></div><div>Cheers,</div><div>Joćo<br><br><div class="gmail_quote">On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter <span dir="ltr"><<a href="mailto:Emanuel.Peter@chemie.uni-regensburg.de" target="_blank">Emanuel.Peter@chemie.uni-regensburg.de</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;"><div style="font-family: Tahoma,sans-serif; font-size: 13px;"><br>Look for the pKa-constants of each part of your system (e.g. each amino-acid). <br>
Then you can check each protonation state and change it according to your<br>application in the force-field.<br><br>Emanuel<br><br>>>> fancy2012 <u></u> 06.09.11 13.01 Uhr >>><br>
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Dear gmx users,<br><br>Are there some tutorials on constant PH simulations using gromacs? How should I state my work? Right now I have no idea on it.<br><br></div><div>--<div><br><p align="left"><u>Best wishes,</u></p>
<p align="left"><u>Qinghua Liao</u></p>
<p align="left"><u>Ph.D student of Tianjin University, China</u></p></div></div></div><u></u></div>
<br>--<br>
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PhD Student<br>Protein Modelling Group<br>ITQB-UNL, Oeiras, Portugal<br>Tel:<a href="tel:%2B351-214469613" value="+351214469613" target="_blank">+351-214469613</a><br>
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<u></u></div></div></div>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Joćo M. Damas<br>
PhD Student<br>Protein Modelling Group<br>ITQB-UNL, Oeiras, Portugal<br>Tel:+351-214469613<br>
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