[gmx-users] CHARMM36 force field available for GROMACS

[rajat desikan]

Thank you, Justin.
I am particularly interested in the lipid simulations. Can you upload the
final results on dropbox? Sorry for the trouble...I intend to simulate a
membrane-protein system using charmm36. I will let you know how that goes.
Thanks.


On Wed, Oct 9, 2013 at 5:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/9/13 7:03 AM, rajat desikan wrote:
>
>> Superb stuff, Justin. Thank you so much. Is it asking too much for a brief
>> list of the test systems that you used? Thanks again.
>>
>>
> We tested everything, at least in terms of representative examples.
>  Single amino acids, full proteins in vacuo, single nucleotides,
> full-length ssRNA and dsDNA, individual lipids with and without water and
> ions, proteins in solution with ions, and a wide variety of small molecules
> interacting with each other. Everything came out in agreement between the
> two programs, including everything that utilized NBFIX terms.
>
> -Justin
>
>
>> On Wed, Oct 9, 2013 at 1:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> All,
>>>
>>> I am pleased to announce the immediate availability of the latest
>>> CHARMM36
>>> force field in GROMACS format.  You can obtain the archive from our lab's
>>> website at http://mackerell.umaryland.****edu/CHARMM_ff_params.html<http
>>> **://mackerell.umaryland.edu/**CHARMM_ff_params.html<http://mackerell.umaryland.edu/CHARMM_ff_params.html>
>>> >
>>>
>>> .
>>>
>>> The present version contains up-to-date parameters for proteins, nucleic
>>> acids, lipids, some carbohydrates, CGenFF version 2b7, and a variety of
>>> of
>>> other small molecules.  Please refer to forcefield.doc, which contains a
>>> list of citations that describe the parameters, as well as the CHARMM
>>> force
>>> field files that were used to generate the distribution.
>>>
>>> We have validated the parameters by comparing energies of a wide variety
>>> of molecules within CHARMM and GROMACS and have found excellent agreement
>>> between the two.  If anyone has any issues or questions, please feel free
>>> to post them to this list or directly to me at the email address below.
>>>
>>> Happy simulating!
>>>
>>> -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