<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:12pt"><div>Thanks for your response.<br><br>While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here:<br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;"><span><a target="_blank" href="http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html">http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html</a></span><br><br>Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules?<br><br>The main thing that I am still unsure about is how the previously mentioned paper converted the
sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process.<br><br>Regards,<br>Reza Salari<br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Andrew Paluch <apaluch@nd.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Tue, December 15, 2009 4:34:18 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] New ion parameters and OPLS-AA<br></font><br>
Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly,<br><br>Andrew<br><br><div class="gmail_quote">
On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari <span dir="ltr"><<a rel="nofollow" ymailto="mailto:resal81@yahoo.com" target="_blank" href="mailto:resal81@yahoo.com">resal81@yahoo.com</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><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;">
<div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;">Hi All,<br><br>Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas.<br>
<br>However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is
here:<br><span><span><a target="_blank" href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000130000012124507000001&idtype=cvips&gifs=Yes">http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000130000012124507000001&idtype=cvips&gifs=Yes</a></span></span><br>
<br>In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other.<br>
<br>So does anyone know if there is such way? Does GROMACS internally treats sigmas as "sigma prime" for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on
clarifying this.<br><br>Regards,<br><font color="#888888">Reza Salari<br></font></div></div></div><br>--<br>
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