jalemkul at vt.edu
Thu Oct 24 15:07:21 CEST 2013
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
> 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
>>> 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 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
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul, Ph.D.
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 | (410) 706-7441
More information about the gromacs.org_gmx-users