<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:12pt"><div>Thank you very much. That sounds interesting!<br><br>BTW, I finally found out that the only way to use parameters developed using different combination rules together, is to define them manually in nonbonding_params section of topology. This sounds a little bit dangerous since it is sort of mixing different approaches.<br><br>Regards,<br>Reza Salari<br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Alexandre Suman de Araujo <asaraujo@if.sc.usp.br><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight: bold;">Sent:</span></b> Wed, December 16, 2009
11:36:50 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] New ion parameters and OPLS-AA<br></font><br>
If you decide to change the ions parameters, you can use the method described here:<br><br><span><a target="_blank" href="http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255D&searchHistoryKey">http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255D&searchHistoryKey</a>=</span><br><br>It is relatively fast and provide nice parameters.<br><br>Cheers<br><br>--Alexandre Suman de Araujo<br>Instituto de Física de São Carlos<br>Universidade de São Paulo<br>São Carlos - Brasil<br><br><br>Citando Reza Salari <<a ymailto="mailto:resal81@yahoo.com" href="mailto:resal81@yahoo.com">resal81@yahoo.com</a>>:<br><br>> 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>> <br><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>> <br>> <br>> ________________________________<br>> From: Andrew Paluch <<a ymailto="mailto:apaluch@nd.edu" href="mailto:apaluch@nd.edu">apaluch@nd.edu</a>><br>> To: Discussion list for GROMACS users <<a
ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Tue, December 15, 2009 4:34:18 PM<br>> Subject: Re: [gmx-users] New ion parameters and OPLS-AA<br>> <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>> <br>> On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari <<a ymailto="mailto:resal81@yahoo.com" href="mailto:resal81@yahoo.com">resal81@yahoo.com</a>> wrote:<br>> <br>> 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<br>>> here:<br><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><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<br>>> clarifying this.<br>>> <br>>> Regards,<br>>> Reza Salari<br>>> <br>>> --<br>>>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><span>>> <a target="_blank"
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