Re: [gmx-users] Gromos54a8
Dear Rajat Desikan, I recently ported the 54A8 to Gromacs format. However I did not have the time yet to extensively test it or compare it to published results. I did the porting by hand (the differences between 54A7 and 54A8 are modest), which is of course more error prone. I'll send you the files off list. If you would want to check and test them, that would be of great value for me too. And after that the force field could of course be shared with the greater Gromacs community. Groetnis, Djurre H. de Jong, PhD Theory of complex systems group Westfällische Wilhelms-Universität Münster On Thursday, 24 October 2013, 15:18, rajat desikan rajatdesi...@gmail.com wrote: Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgz**http**://www.gromacs.org/@api/** deki/**files/74/= http://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzht**tp://www.gromacs.org/@api/** deki/files/74/=**ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing list gmx-users@gromacs.org
Re: [gmx-users] Gromos54a8
Thank you so much, Djurre. I will do some tests with protein-membrane systems in mind and share it with the community. I will see if I can reproduce the results in the 54A8 paper. On Fri, Oct 25, 2013 at 1:01 PM, Djurre de Jong-Bruinink djurredej...@yahoo.com wrote: Dear Rajat Desikan, I recently ported the 54A8 to Gromacs format. However I did not have the time yet to extensively test it or compare it to published results. I did the porting by hand (the differences between 54A7 and 54A8 are modest), which is of course more error prone. I'll send you the files off list. If you would want to check and test them, that would be of great value for me too. And after that the force field could of course be shared with the greater Gromacs community. Groetnis, Djurre H. de Jong, PhD Theory of complex systems group Westfällische Wilhelms-Universität Münster On Thursday, 24 October 2013, 15:18, rajat desikan rajatdesi...@gmail.com wrote: Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgz**http**://www.gromacs.org/@api/** deki/**files/74/= http://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzht**tp://www.gromacs.org/@api/** deki/files/74/=**ConvertGromos2Gromacs.tgz http://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A.
[gmx-users] Gromos54a8
Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgzin the user contributions, I do not see any other relevant scripts. Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Gromos54a8
On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgzin the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Gromos54a8
Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp**://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Gromos54a8
On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp**://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Gromos54a8
Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgz**http**://www.gromacs.org/@api/** deki/**files/74/= http://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzht**tp://www.gromacs.org/@api/** deki/files/74/=**ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] GROMOS54A8 parameters in GROMACS format
Dear Stephane Abel, Theres a link I on the gromacs web site to ATB, or you can google it. If it is not in Gromacs format you can just write a couple 6 liner scripts to re-format it by parsing into the gromacs format, Stephan Watkins Original-Nachricht Datum: Wed, 13 Feb 2013 21:25:33 + Von: ABEL Stephane 175950 stephane.a...@cea.fr An: gmx-users@gromacs.org gmx-users@gromacs.org Betreff: [gmx-users] GROMOS54A8 parameters in GROMACS format Hello all, Does somebody know where i can find the latest GROMOS force field (i.e. GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ? [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247−1264 doi: http://pubs.acs.org/doi/citedby/10.1021/ct300156h Thank you Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] GROMOS54A8 parameters in GROMACS format
Thanks Berk, I have found the script, I will try them Best Stephane Message: 4 Date: Thu, 14 Feb 2013 13:53:56 +0100 From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: dub124-w200b8c2eb085c78933a9418e...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Hi, There are two scripts make_gromos_rtp in the scripts directory which were used to convert Gromos AA topologies to rtp entries. Cheers, Berk From: stephane.a...@cea.fr To: gmx-users@gromacs.org Date: Thu, 14 Feb 2013 11:34:59 + Subject: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format Hello, Yeap, I have seen the links on ATB. Indeed, the conversion of the bonded terms (in this file 54a8.ifp ?) will be not too hard, but it is not the case for the AA topology where several changes were done. So any help will be appreciate.. Stephane -- Message: 5 Date: Thu, 14 Feb 2013 11:18:17 +0100 From: lloyd riggs lloyd.ri...@gmx.ch Subject: Re: [gmx-users] GROMOS54A8 parameters in GROMACS format To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20130214101817.72...@gmx.net Content-Type: text/plain; charset=utf-8 Dear Stephane Abel, Theres a link I on the gromacs web site to ATB, or you can google it. If it is not in Gromacs format you can just write a couple 6 liner scripts to re-format it by parsing into the gromacs format, Stephan Watkins Original-Nachricht Datum: Wed, 13 Feb 2013 21:25:33 + Von: ABEL Stephane 175950 stephane.a...@cea.fr An: gmx-users@gromacs.org gmx-users@gromacs.org Betreff: [gmx-users] GROMOS54A8 parameters in GROMACS format Hello all, Does somebody know where i can find the latest GROMOS force field (i.e. GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ? [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247???1264 doi: http://pubs.acs.org/doi/citedby/10.1021/ct300156h Thank you Stephane -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 106, Issue 73 ** -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Message: 5 Date: Thu, 14 Feb 2013 08:01:43 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] different springs - WHAM To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 511ce037.5020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/13/13 5:23 PM, Steven Neumann wrote: On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/13 9:57 AM, Steven Neumann wrote: On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/13 9:40 AM, Steven Neumann wrote: Dear Gmx Users, I know it is possible to combine windows with different spring constants into the one PMF curve using g_wham. Do I have to somehow tell g_wham that one or two windows have different spring constants? No, they are read from the .tpr files. For instance - I got the better histogram overlap with lower force constant in one window. When I replace this window into the window with the sring constant like all windwos (worse overlap) both PMF curves differ app. 2kcal/mol which is around 30% of the overall deltaG. Is there any error I should inroduce when one window differ in terms of k1? What does g_wham's error analysis suggest? -Justin In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol Seems like a good result, so what's the problem? -Justin That the better overlap of histograms produce worse deltaG comparing to experiment. With all the same spring constants I get the experimental value of deltaG but there is a poor overlap. There must be (somehow) a correction added to deltaG when introdcuing windows with different spring constants. The code and/or g_wham paper should address this. In principle, WHAM can be conducted with any assortment of spring constants you like. If you track down a bug or something, please report it on redmine.gromacs.org. A workaround of course would be to simply add another window (or windows) with the same original force constant that gives adequate sampling. -Justin
[gmx-users] GROMOS54A8 parameters in GROMACS format
Hello all, Does somebody know where i can find the latest GROMOS force field (i.e. GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ? [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247−1264 doi: http://pubs.acs.org/doi/citedby/10.1021/ct300156h Thank you Stephane-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
