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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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