[gmx-users] Gromos54a8

Sun Jul 26 01:36:17 CEST 2015

Hi,
Have you any success with testing the Gromos 54a8 FF in gromacs format? And can you share it? Or can I help somehow with the testing against paper results?
Thanks.

Milan
On Fri, Oct 25, 2013 at 01:33:39PM +0530, rajat desikan wrote:
> 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 <
> djurredejong at 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 <rajatdesikan at 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 <jalemkul at 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 <jalemkul at 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 at outerbanks.umaryland.****edu <jalemkul at outerbanks.**
> > >>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> |
> > >>>> (410) 706-7441
> > >>>>
> > >>>> ==============================****====================
> > >>>>
> > >>>> --
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> > >>>
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> > >>>
> > >> --
> > >> ==============================**====================
> > >>
> > >> 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 at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu>
> > |
> > >> (410) 706-7441
> > >>
> > >> ==============================**====================
> > >> --
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> > >
> > >
> > >
> > >--
> > >Rajat Desikan (Ph.D Scholar)
> > >Prof. K. Ganapathy Ayappa's Lab (no 13),
> > >Dept. of Chemical Engineering,
> > >Indian Institute of Science, Bangalore
> > >
> > >--
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> 
> 
> 
> -- 
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
> --
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