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.tgz<ht**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 list gmx-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/Search<h**ttp://www.gromacs.org/Support/** > >>>> Mailing_Lists/Search< > 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< > http://www.gromacs.org/**Support/Mailing_Lists> > >>>> <http://**www.gromacs.org/Support/**Mailing_Lists< > http://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 > >> http://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/Search< > 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< > http://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 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 > > > > > > > -- > 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 > -- 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 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