Dear Sir, <br><br>Thanks for your reply. I will check it.. <br><br><br><div class="gmail_quote">On Tue, Dec 6, 2011 at 12:26 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Sathish wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Dear all,<br>
<br>
How to run simulation in different PH?<br>
<br>
Kindly help to fix this problem. Thanks in advance...<br>
<br>
</blockquote>
<br></div>
The concept of "pH" is ill-defined for an MD system, the reasons for which have been discussed at length in recent days even (hint: please check the archive before posting). Issues arise with the inability to change protonation, inadequate hydronium parameters, inability to model systems of sufficient size to even achieve a proper pH, and the list goes on.<br>
<br>
The best you might hope for is not a change in "pH" (per strict definition), but rather changing the protonation state of titratable groups in your system according to pKa.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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</font></span></blockquote></div><br><br clear="all"><br>-- <br>-- <br><p style="font-family:arial,helvetica,sans-serif"><font style="font-family:arial,helvetica,sans-serif" size="2">Regards,<br>
N. Sathishkumar,</font></p><br><p style="font-family:arial,helvetica,sans-serif"><font size="2"><a href="mailto:sathish@khu.ac.kr" target="_blank"><br></a></font></p><br>