<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>From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Date: Sun, 20 May 2007 20:59:45 +0200<br>Subject: Re: [gmx-users] pH<br>Dmitriy Golubovsky wrote:
<br>> Dear Guru!<br>><br>> have you got any idea, on what how to calculate pH. for the system?<br>> i'm solving a promblem of coil-globule transition for polymer.<br>> do the topology for my structure(opls ff), do MD in water (spc). get the
<br>> statiscts. everything is ok.<br>> the summary charge is equal to zero. no dissociation.<br>> so the question is - how to calculate pH. or it's not possible?<br>> if it is possible, than how to variate this pH in some range.
<br>><br>> I allready try to use genion, but didn't get good results, on case of<br>> very big dependence of the results from the initial conformations of ions.<br>><br>How about computing the H3O+ concentration?
<br>It is close to impossible to simulate realistic pH with limited size<br>systems. In practice your pH is always seven.<br><br>What do you mean with "no dissociation"?<br><br></blockquote></div>Dear David, <br>
thanks for a quick answer.<br>1. what do you mean, when you say "pH is always seven".<br>2. when I said "dissociation", I mean that, I didn't use Morse potential for the bond, so, for examle, COOH group haven't got probability to break the connectivity with H atom.
<br>3. i haven't got an idea how to calculate H3O+ concentration.<br><br>Thanks.<br><br clear="all"><br>-- <br>Dmitriy Golubovsky