<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 Dr Paluch and Dr van der Spoel for your responses.<br><br>Then it seems it would be safer to use mixing the combination rules as a last
resort, although it is comforting to know that other people have used
it before successfully.<br><br>I think I will look for the parameters that are compatible with the OPLS-AA combination rule. Although based on Horinek paper I was sort of hoping that I could convert the parameters for different combination rules.<br><br>Regards,<br>Reza Salari<br><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> David van der Spoel <spoel@xray.bmc.uu.se><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> Wed, December 16, 2009 3:10:13 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] New ion parameters and OPLS-AA<br></font><br>
On 12/15/09 11:03 PM, Reza Salari wrote:<br>> Thanks for your response.<br>><br>> While I will try that (although it seems it needs quite amount of<br>> scripting), I remember in the past some people in the mailing list<br>> mentioned problems while using nonbond_params directvie with OPLS-AA and<br>> in response it was generally suggested to avoid doing this kind of<br>> mixing. Like Dr Abraham suggestion here:<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<br>> overridden by the default rules?<br>><br>> The main thing that I am still unsure about is how the previously<br>> mentioned paper converted the sigma values for different combination<br>> rules. It seems that there must be a relatively direct
way to do this<br>> without going through the re-parametrization process.<br><br>Unfortunately the combination rules are part of the parameterization, <br>simply because changing the combination rules means changing the <br>parameters. Hence I would suggest you look for ion parameters that are <br>compatible with your force field of choice, alternatively a force field <br>that is compatible with your ions of choice. Since these ion parameters <br>were developed by Tom Cheatham I presume that Amber would be a suitable <br>force field.<br><br>><br>> Regards,<br>> Reza Salari<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<br>> rather than using the same mixing rule for all terms. You can easily<br>> write a script to modify your input files accordingly,<br>><br>> Andrew<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><br>> <mailto:<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<br>> Joung and Chetham and I am interested in running some test runs<br>> using these
parameters. These set of parameters are based on using<br>> LB rule (arithmetic mean) for sigmas.<br>><br>> However I am using OPLS-AA ff so I am using the combination rule 3<br>> (geometric mean of corresponding A and B values). My question is<br>> that can I use the exact sigma values from Cheatham for my<br>> simulations? I'm almost positive that I have to change these sigma<br>> values to be consistent with the combination rule that I am using.<br>> In fact there is a paper by Horinek et al that has a nice table of<br>> different ionic sigma and epsilon values from different parameter<br>> sets (Aqvist, Jensen, Cheatham,..). The article is 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>> <<a href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000130000012124507000001&idtype=cvips&gifs=Yes" target="_blank">http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000130000012124507000001&idtype=cvips&gifs=Yes</a>><br>><br>> In that table, they have mentioned two sigmas; a usual sigma (which<br>> is used with rule 2) and a sigma prime (which can be used with rule<br>> 3). However it seems sort of unclear to me how they got these value<br>> since in some references that they've mentioned I
could find either<br>> sigma or sigma prime, not both. So I am guessing there must be some<br>> way to convert these two sigmas to each other.<br>><br>> So does anyone know if there is such way? Does GROMACS internally<br>> treats sigmas as "sigma prime" for OPLS-AA? I looked at the manual<br>> and also searched the mailing list to find an explanation but<br>> without luck. I really appreciate any help on 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>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><span>> <a
target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>> Please search the archive at <a target="_blank" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before</span><br>> posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br><span>> Can't post? Read <a target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></span><br>><br>><br><br><br>--
<br>David van der Spoel, Ph.D., Professor of Biology<br>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br><a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a ymailto="mailto:spoel@gromacs.org" href="mailto:spoel@gromacs.org">spoel@gromacs.org</a><span> <a target="_blank" href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a></span><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><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before
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