[gmx-users] Gromos54a8

[Justin Lemkul]

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/=
>>> **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> |
>> (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 | (410) 706-7441

==================================================