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

[Justin Lemkul]

On 1/23/16 10:25 AM, Alexander Alexander wrote:
> 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.
>

No, you don't need to freeze anything. The single-point evaluation, if done 
correctly (as stated in the previous links) does not change the coordinates, it 
merely evaluates the energy for the provided configuration.  I don't know that 
it will do any harm, but freezing is a very unphysical perturbation that is not 
necessary to achieve your goal.

-Justin

> 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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-- 
==================================================

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

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