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.tgz<http**://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 <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