Re: [gmx-users] New ion parameters and OPLS-AA
On 12/15/09 11:03 PM, Reza Salari wrote: Thanks for your response. 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: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? 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. Unfortunately the combination rules are part of the parameterization, simply because changing the combination rules means changing the parameters. Hence I would suggest you look for ion parameters that are compatible with your force field of choice, alternatively a force field that is compatible with your ions of choice. Since these ion parameters were developed by Tom Cheatham I presume that Amber would be a suitable force field. Regards, Reza Salari *From:* Andrew Paluch apal...@nd.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, December 15, 2009 4:34:18 PM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA 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, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, 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. 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: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes 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. 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. Regards, Reza Salari -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Thank you very much Dr Paluch and Dr van der Spoel for your responses. 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. 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. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, December 16, 2009 3:10:13 AM Subject: Re: [gmx-users] New ion parameters and OPLS-AA On 12/15/09 11:03 PM, Reza Salari wrote: Thanks for your response. 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: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? 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. Unfortunately the combination rules are part of the parameterization, simply because changing the combination rules means changing the parameters. Hence I would suggest you look for ion parameters that are compatible with your force field of choice, alternatively a force field that is compatible with your ions of choice. Since these ion parameters were developed by Tom Cheatham I presume that Amber would be a suitable force field. Regards, Reza Salari *From:* Andrew Paluch apal...@nd.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, December 15, 2009 4:34:18 PM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA 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, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, 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. 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: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes 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. 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. Regards, Reza Salari -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala
Re: [gmx-users] New ion parameters and OPLS-AA
Thank you very much. That sounds interesting! 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. Regards, Reza Salari From: Alexandre Suman de Araujo asara...@if.sc.usp.br To: gmx-users@gromacs.org Sent: Wed, December 16, 2009 11:36:50 AM Subject: Re: [gmx-users] New ion parameters and OPLS-AA If you decide to change the ions parameters, you can use the method described here: http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey= It is relatively fast and provide nice parameters. Cheers --Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Citando Reza Salari resa...@yahoo.com: Thanks for your response. 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: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? 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. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA 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, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, 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. 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: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes 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. 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. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Novo Webmail IFSC -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] New ion parameters and OPLS-AA
Thank you very much. That sounds interesting! 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. NO don't do that! You will not be using the same parameters, if you change the combination rules. Regards, Reza Salari *From:* Alexandre Suman de Araujo asara...@if.sc.usp.br *To:* gmx-users@gromacs.org *Sent:* Wed, December 16, 2009 11:36:50 AM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA If you decide to change the ions parameters, you can use the method described here: http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey= It is relatively fast and provide nice parameters. Cheers --Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Citando Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com: Thanks for your response. 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: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? 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. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu mailto:apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA 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, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, 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. 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: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes 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. 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. Regards, Reza Salari -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Novo Webmail IFSC -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman
Re: [gmx-users] New ion parameters and OPLS-AA
Thanks for your response. So basically since the Cheatham parameters are using LB rule, I can never use them with OPLS-AA? 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). 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. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, December 16, 2009 1:08:58 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Thank you very much. That sounds interesting! 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. NO don't do that! You will not be using the same parameters, if you change the combination rules. Regards, Reza Salari *From:* Alexandre Suman de Araujo asara...@if.sc.usp.br *To:* gmx-users@gromacs.org *Sent:* Wed, December 16, 2009 11:36:50 AM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA If you decide to change the ions parameters, you can use the method described here: http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey= It is relatively fast and provide nice parameters. Cheers --Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Citando Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com: Thanks for your response. 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: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? 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. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu mailto:apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA 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, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, 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. 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: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes 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
[gmx-users] New ion parameters and OPLS-AA
Hi All, 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. 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: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes 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. 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. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
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, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, 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. 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: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes 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. 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. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Thanks for your response. 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: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? 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. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA 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, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, 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. 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: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes 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. 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. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Hi Reza, -- Message: 4 Date: Tue, 15 Dec 2009 14:03:36 -0800 (PST) From: Reza Salari resa...@yahoo.com Subject: Re: [gmx-users] New ion parameters and OPLS-AA To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 858209.12986...@web35303.mail.mud.yahoo.com Content-Type: text/plain; charset=us-ascii Thanks for your response. 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: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? I have successfully done so. My topology looks like this: #include ffoplsaa.itp [ nonbond_params ] opls_272 opls_412 1 0.277 1.2857 #include frm.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif . . . Of course there should be a line for every possible pair interaction. It is important to put the [ nonbond_params ] after the include to ffoplsaa.itp 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. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA 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, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, 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. 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: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes 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. 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. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
