[gmx-users] atomtypes

[Alexander Alexander]

Do you know please any source for them by chance?
The best,

On Wed, Apr 20, 2016 at 8:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>
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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
>
> ==================================================
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