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

[Alexander Alexander]

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?

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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