[gmx-users] Gromos54a8

Fri Oct 25 09:31:46 CEST 2013

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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