[gmx-users] atomtypes

[Justin Lemkul]

On 4/20/16 2:01 PM, Alexander Alexander wrote:
> Thanks.
> Then no matter which program or package has been used to drive them? then I
> can take them and use in Gromacs.

A force field is a force field, as long as the functional form is supported by 
GROMACS you can use it.

> Also,
> No matter if they have been derived for a bulk crystal of the element or
> its surface or even a complex molecule?

I don't do simulations of such systems, but in general, no, you can't make such 
an assumption.

-Justin

> Cheers,
> Alex
>
> On Wed, Apr 20, 2016 at 7:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/20/16 1:50 PM, Alexander Alexander wrote:
>>
>>> Dear GMXuser,
>>>
>>> Suppose  I have the *.gro file for the (111) surface of for example Ni or
>>> Pt or Au, then, I was wondering that where I can find the required
>>> information in [ atomtypes ] section for this surface, especially sigma
>>> and
>>> epsilon?
>>>
>>> [ atomtypes ]
>>> ;   name      mass        charge    ptype       sigma      epsilon
>>>        Ni          58.69            0            A              ?
>>>      ?
>>>
>>>
>> If there's not already a published, reliable force field, you have to
>> derive one yourself.  The LJ terms are often the hardest.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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