<div>Hi Tanos,</div>
<div> </div>
<div>Perhaps you should try one of the available constant-pH MD methods. Here is a quick explanation of what they do and who is involved in their development right now:</div>
<div> </div>
<div><a href="http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation">http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation</a><br></div>
<div>My opinion regarding this subject may be a little biased since I've worked with one of the most active researchers in this area, but I would suggest you to read some papers from Antonio Baptista and/or<font color="#000000"> Miguel Machuqueiro (from Baptista's 2002 initial "Constant-pH molecular dynamics using stochastic titration" paper to nowadays).</font></div>
<div> </div>
<div>Best regards,</div>
<div> </div>
<div class="gmail_quote">On Tue, May 10, 2011 at 7:22 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br><br>Tanos Celmar Costa Franca wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>Dear GROMACS users,<br>Does someone now how to procede to change the pH of a MD simulation from the physiologic one (7.4) to 6.5 ?<br>
<br></blockquote><br></div>Classical MD simulations do not currently allow for dynamic proton exchange. The best you can do at the moment is use pdb2gmx to set the protonation state of titratable residues. At pH 6.5, histidines will be quite annoying to deal with properly.<br>
<br>-Justin
<div class="im"><br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>Tanos Celmar Costa Franca - D.Sc<br>Coordenador do Programa de Pos-graduacão em Química<br>Secão de Engenharia Química - SE/5<br>
Instituto Militar de Engenharia - IME<br>Rio de Janeiro - RJ<br>Brasil<br><br><br><br><br><br>----------------------------------------------------------------<br>This message was sent using IMP, the Internet Messaging Program.<br>
<br></blockquote><br>-- <br></div>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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