[gmx-users] Gromos54a8

[rajat desikan]

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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> >>>
> >> --
> >> ==============================**====================
> >>
> >> 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