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
