[gmx-users] A simple question

Mark Abraham mark.j.abraham at gmail.com
Wed May 10 23:00:11 CEST 2017 

Hi,

You're also double counting a bunch of kinetic energy in (1).

Each particle can have an interaction with every other particle, and you
can count it only once. Each particular has a kinetic energy, and you can
count it only once.

Mark

On Wed, May 10, 2017 at 10:48 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/10/17 4:41 PM, Alex wrote:
> > Here are the results, p,s and w are representing a peptide, solid surface
> > and water, respectively.
> >
> > Utot = -1340400
> >
> > us = -1.0173e+06
> > uw = -382847
> > up = -805.9
> > usw = -1.42594e+06
> > ups = -1.0189e+06
> > upw = -385347
>
> You're definitely getting double-counting here with the intramolecular
> nonbonded
> interactions.  Note that both usw and ups are nearly the same as Utot.  The
> total energy of a solid-water and peptide-solid system will have such
> overlap.
> The total of us + uw + up + (nonbonded energy *only* between usp, ups, upw)
> should roughly sum to Utot.
>
> -Justin
>
> >
> > one combination: (1) \sum uxy = us + uw + up + usw + ups + upw =
> > -4231139.9  --> \Delta = + 2890739.9
> >
> > I though that the each of us, uw, up, are being double counted in the
> (1),
> >
> > So, I subtracted out them in (2), the result is a bit closer, but still:
> >
> > (2) : us + uw + up + usw + ups + upw - 2*(us + uw + up) = -1429234.10
>  -->
> > \Delta = + 88834.10
> >
> > Although, there is also a single Na counter-ion in the soup, but the
> effect
> > if that can not really compensate the difference: (u_ion = -13.5205 and
> > u_ionp = -827.121)
> >
> > In general what should be the right relation between the total internal
> > energy of a system and internal energies of its constructive segments?
> >
> > Thanks
> > Alex
> >
> > On Wed, May 10, 2017 at 10:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 5/10/17 4:14 PM, Alex wrote:
> >>
> >>> Hi Justin,
> >>>
> >>> Thanks for response.
> >>> But all my energy are contain both kinetic and potential energies.
> >>>
> >>> In "gmx energy ...", I just chose the "Total-Energy" for calculation of
> >>> the
> >>> energies (total energy of the whole system and other U_A, U_B ...),
> and as
> >>> far as I know in the NVT ensemble, the "Total-Energy" is the sum of
> both
> >>> kinetic and potential energies.
> >>>
> >>> I mean in gmx energy ...
> >>> .....         8  Disper.-corr.
> >>>   9  Coulomb-(SR)    10  Coul.-recip.    11  Position-Rest.  12
> Potential
> >>>  13  Kinetic-En.     14  Total-Energy ...
> >>>
> >>> which I invoked separately for each part ... and two by two .., the
> >>> Total-Energy
> >>> = Potential + Kinetic-En as I tested it.
> >>>
> >>>
> >> How different are the values?  Anything obvious about the value of the
> >> difference?  We'll need to see some real numbers here.
> >>
> >> -Justin
> >>
> >>
> >> Regards,
> >>> Alex
> >>>
> >>>
> >>>
> >>> On Wed, May 10, 2017 at 10:03 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >>>
> >>>
> >>>>
> >>>> On 5/10/17 3:41 PM, Alex wrote:
> >>>>
> >>>> Hello gromacs user,
> >>>>>
> >>>>> Out of a well converged NVT simulation, I calculated the
> "Total-Energy =
> >>>>> Utot" as total internal energy of the system which contain three
> pieces
> >>>>> (A,
> >>>>> B and water).
> >>>>> Then, using "gmx trjconv" and "gmx mdrun -rerun", "gmx energy", I
> >>>>> calculated the "Total-Energy" of each piece as U_A, U_B and U_W,
> using
> >>>>> the
> >>>>> same method, I calculate again the U_AB, U_AB, U_AW ... , which is
> the
> >>>>> internal energy due to interaction between two pieces in the soup.
> >>>>>
> >>>>> I expected that summing over U_A, U_B and U_W, U_AB ...., give me the
> >>>>> "Total-Energy
> >>>>> = Utot" of the system, but no combination of U_A, U_B and U_W, U_AB
> ...
> >>>>> could be equal to the "Total-Energy = Utot" !and the difference is
> >>>>> really
> >>>>> considerable.
> >>>>>
> >>>>> Would you please let me know why so? or I am doing wrong somewhere?
> >>>>>
> >>>>>
> >>>>> Total energy is the sum of kinetic and potential energy.  No
> combination
> >>>> of only potential energy terms will give the total energy.  They
> should
> >>>> sum
> >>>> (within reasonable numeric precision) to the potential energy of the
> >>>> whole
> >>>> system.
> >>>>
> >>>> -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
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
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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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> Gromacs Users mailing list
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