[gmx-users] Gromos54a8

[rajat desikan]

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