[gmx-users] computation of energy for energygrps + problem using g_enemat

[Justin Lemkul]

On 8/31/15 10:33 AM, ANTHONY C MANSON wrote:
> Hello:
> energy for energygrps:I am trying to estimate the polar solvation energy of a
> 76 residueprotein at standard conditions.  I am using the gromacs 4.5.3 dp
> release.  I have set up a simulation with the solvated  (using spce water)
> protein.I have defined two energygrps: Protein SOL in the *.mdp file.  I have
> run the simulation and have then run g_energy on the *.edr file.  I get the
> following choices from g_energy:
>    1  Bond             2  Angle            3  Proper-Dih.      4  Improper-Dih.
>   5  LJ-14            6  Coulomb-14       7  LJ-(SR)          8  Disper.-corr.
> 9  Coulomb-(SR)    10  Coul.-recip.    11  Potential       12  Kinetic-En.
> 13  Total-Energy    14  Temperature     15  Pres.-DC        16  Pressure
> 17  Vir-XX          18  Vir-XY          19  Vir-XZ          20  Vir-YX
> 21  Vir-YY          22  Vir-YZ          23  Vir-ZX          24  Vir-ZY
> 25  Vir-ZZ          26  Pres-XX         27  Pres-XY         28  Pres-XZ
> 29  Pres-YX         30  Pres-YY         31  Pres-YZ         32  Pres-ZX
> 33  Pres-ZY         34  Pres-ZZ         35  #Surf*SurfTen   36  Mu-X
> 37  Mu-Y                                38  Mu-Z
> 39  Coul-SR:Protein-Protein             40  LJ-SR:Protein-Protein
> 41  Coul-14:Protein-Protein             42  LJ-14:Protein-Protein
> 43  Coul-SR:Protein-SOL                 44  LJ-SR:Protein-SOL
> 45  Coul-14:Protein-SOL                 46  LJ-14:Protein-SOL
> 47  Coul-SR:SOL-SOL                     48  LJ-SR:SOL-SOL
> 49  Coul-14:SOL-SOL                     50  LJ-14:SOL-SOL
> 51  T-System
> I pick Coul-SR:Protein-SOL as a component of the polar solvation energy.I note
> that the energy magnitude seems extremely high:
> Energy                      Average   Err.Est.       RMSD
> Tot-Drift-------------------------------------------------------------------------------Coul-SR:Protein-SOL        -8343.86         46    193.457    -192.93  (kJ/mol)
> This seems unreasonable to me.  I wanted to understand how mdrun was calculating this value.  Perhaps it is accumulating energies overmany frames.  What part of the code (force.c ...) handles thiscalculation so I can verify its action and assess whether these numbersare useful.

It's not an accumulated value; it's an average.  Confirm with the time series 
printed as a result of your g_energy command.

> g_enemat:Also, I tried running g_enemat on this with the following groups.dat file.
> 2ProteinSOL
> I use the command:
> g_enemat  -f ub_short.edr -e 100
> and get:
> Opened ub_short.edr as double precision energy fileWill read groupnames from inputfileRead 2 groupsgroup 0WARNING! could not find group (null):Protein-Protein (0,0)in energy fileWARNING! could not find group (null):Protein-SOL (0,1)in energy filegroup 1WARNING! could not find group (null):SOL-SOL (1,1)in energy file
> Will select half-matrix of energies with 6 elementsRead frame: 1000, Time: 100.000e  100.000         Will build energy half-matrix of 2 groups, 6 elements, over 1001 framesSegmentation fault
>

Many problems have been reported with g_enemat, especially in an ancient version 
like the one you're using.  It won't give you anything useful, anyway.

-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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