<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>So basically since the Cheatham parameters are using LB rule, I can never use them with OPLS-AA? <br><br>I was thinking if I find the parameters for OPLS atoms that are based on geometric rule (if there such a thing exists at all), I could use them along with Cheatham parameters and then define the hetero-atomic LJ parameters in nonbonding_params section. This way I would be mixing parameters that have been developed the same way (regarding combination rules).<br><br>I understand that one shouldn't directly mix the sigma's that have been developed using different combination rules. If I there is no OPLS parameters based on LB rule, as you mentioned I have to switch to some ff like Amber.<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> 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 1:08:58 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] New ion parameters and OPLS-AA<br></font><br>
> <br>> 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>NO don't do that! You will not be using the same parameters, if you change the combination rules.<br><br>> <br>> Regards,<br>> Reza Salari<br>> <br>> ------------------------------------------------------------------------<br>> *From:* Alexandre Suman de Araujo <<a ymailto="mailto:asaraujo@if.sc.usp.br" href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>><br>> *To:* <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> *Sent:* Wed, December 16, 2009 11:36:50 AM<br>> *Subject:* Re: [gmx-users] New ion parameters
and OPLS-AA<br>> <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><a href="http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255D&searchHistoryKey" target="_blank">http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255D&searchHistoryKey</a>>=<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> <mailto:<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> <mailto:<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> <mailto:<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> <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 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><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 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> <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 posting!</span><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"
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Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before 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> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>-- David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Professor of Biology<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala,
Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<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://xray.bmc.uu.se/%7Espoel">http://xray.bmc.uu.se/~spoel</a></span><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><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 posting!<br>Please don't post (un)subscribe
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