[gmx-users] Energy profile of a single water molecule on Ni surface

[Alexander Alexander]

What I want is the ADSORPTION energy of water on the surface versus the
vertical DISTANCE of water on the surface. So, I think the single-point
energy is the right case for me, but I think I have to freeze the surface
as well.

On Sat, Jan 23, 2016 at 4:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/23/16 10:06 AM, Alexander Alexander wrote:
>
>> Thank you Justin.
>>
>> My primaraly case.mdp file is below, would you please have a look to see
>> everything is fine beside of energygrps to get what I want to calculate.
>>
>> Meanwhile, I also red something about single point energy calculation
>> using
>> "mdrun -s input.tpr -rerun configuration.pdb" referred by this link
>>
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-August/100166.html
>> So,  where this stand respect to what I am desiring?
>>
>>
> If all you want is the interaction energy for some fixed configuration,
> then it's really easy.  You just define energygrps as needed and calculate
> the energy of that configuration.  For more, see
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
> If you want to calculate the energy over time for some dynamics
> simulation, then just add energygrps. I don't know why you would be
> freezing water (allowing the surface to move but not the water?) but that's
> all up to you in terms of your experimental design.  The interaction energy
> itself is trivial.
>
> -Justin
>
>
> water-ni.mdp
>> +++++++++++++++
>> integrator = md
>> dt = 0.001 ; ps
>> nsteps = 1000000 ; = 0.5 ns tot
>> nstcomm = 10
>> nstxout = 0
>> nstvout = 0
>> nstfout = 0
>> nstlog = 10000
>> nstenergy = 500
>> nstxtcout= 100
>>
>> nstlist = 10
>> ns_type = grid
>> coulombtype =cutoff
>> rcoulomb = 1.0
>> vdwtype = cutoff
>> rvdw = 1.0
>>
>> ;Couplig Temp
>> tcoupl = v-rescale
>> tau_t = 0.1
>> tc-grps = System
>> ref_t = 298
>>
>> ;Costrain Bond
>> constraints = all-bonds
>> constraint_algorithm = LINCS
>>
>> ;Coupling P
>> Pcoupl = no
>> Pcoupltype = isotropic
>> tau_p = 1
>> compressibility = 4.5e-5
>> ref_p=1
>>
>> ;Generate velocity
>> gen_vel = no
>> gen_temp = 298.0
>> gen_seed = 173529
>> cutoff-scheme = Verlet
>>
>> ;Freezing
>> freezegrps = SOL
>> freezedim = Y Y Y
>> ++++++++++++++++++
>>
>> On Sat, Jan 23, 2016 at 3:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 1/23/16 9:16 AM, Alexander Alexander wrote:
>>>
>>> Dear Gromacs user,
>>>>
>>>> I am a new user trying to produce the energy profile of a single water
>>>> molecule on Ni(111) surface, I mean adsorption energy of water molecule
>>>> on
>>>> surface VS the distance of the molecule to surface. The goal is to
>>>> compare
>>>> such a profile with the same profile out of DFT.
>>>>
>>>> Adsorption energy in DFT is defined as:
>>>>    {Ad_energy = [Total energy_(water-surface)] -  [Total
>>>> energy_(surface)]
>>>> -
>>>> [Total energy_(water)]}
>>>>
>>>> How can I calculate the adsorption energy in MD - gromacs? Which one I
>>>> should choose out of "gmx energy -f case.edr ....?  "Total-Energy" or
>>>> "LJ-(SR)" or Potential energy ... .
>>>>
>>>> After lots of effort navigating the gromacs manual I could manage the
>>>> attached inputs file for my calculations, but to be honest,  I really
>>>> don't
>>>> know how my results are reliable. So, to improve my input files and
>>>> comment
>>>> and suggestion are highly welcome.
>>>>
>>>>
>>>> The mailing list does not accept attachments.  Obtaining what you want
>>> is
>>> easy:
>>>
>>> energygrps = surface water
>>>
>>> in the .mdp file will do it.  Whether or not that's anywhere close to the
>>> DFT result depends on the force field and how it was parametrized.
>>>
>>> -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
>
> ==================================================
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