[gmx-users] Potential energy of the prot. only

[pascal.baillod at epfl.ch]

Hello,

I am trying to compute the potential energy of the protein of my system
simulated in explicit spc water. I have the energy groups protein and other and
am trying to figure out whcih terms of the g_energy output I should sum up to
get the proteins total potential energy (without interactions with the solvent).
 To me the terms 1 4 3 4 46 47 48 0 make most sense and give the result here
below for the trpc (a 20 residue peptide in a half folded conformation). I
assume term 49 (49=Coul-14:Protein-Protein) is already counted in term 46
(=Coul-SR:Protein-Protein) and 48 (=Coul-LR:Protein-Protein). Similarily, 50 is
already counted in 47, I suppose..



End your selection with 0
   1=       G96Bond   2=      G96Angle   3=   Proper Dih.   4= Improper Dih.
   5=         LJ-14   6=    Coulomb-14   7=       LJ (SR)   8=  Coulomb (SR)
   9=  Coulomb (LR)  10=     Potential  11=   Kinetic En.  12=  Total Energy
  13=   Temperature  14=Pressure (bar)  15=         Box-X  16=         Box-Y
  17=         Box-Z  18=        Volume  19=  Density (SI)  20=            pV
  21=        Vir-XX  22=        Vir-XY  23=        Vir-XZ  24=        Vir-YX
  25=        Vir-YY  26=        Vir-YZ  27=        Vir-ZX  28=        Vir-ZY
  29=        Vir-ZZ  30= Pres-XX (bar)  31= Pres-XY (bar)  32= Pres-XZ (bar)
  33= Pres-YX (bar)  34= Pres-YY (bar)  35= Pres-YZ (bar)  36= Pres-ZX (bar)
  37= Pres-ZY (bar)  38= Pres-ZZ (bar)  39= #Surf*SurfTen  40=  Pcoupl-Mu-XX
  41=  Pcoupl-Mu-YY  42=  Pcoupl-Mu-ZZ  43=          Mu-X  44=          Mu-Y
  45=          Mu-Z  46=Coul-SR:Protein-Protein  47=LJ:Protein-Protein 
48=Coul-LR:Protein-Protein
  49=Coul-14:Protein-Protein  50=LJ-14:Protein-Protein  51=Coul-SR:Protein-Other
 52=LJ:Protein-Other
  53=Coul-LR:Protein-Other  54=Coul-14:Protein-Other  55=LJ-14:Protein-Other 
56=Coul-SR:Other-Other
  57=LJ:Other-Other  58=Coul-LR:Other-Other  59=Coul-14:Other-Other 
60=LJ-14:Other-Other
  61=     T-Protein  62=       T-Other  63=  Lamb-Protein  64=    Lamb-Other
1 4 3 4 46 47 48 0
 
Back Off! I just backed up test.xvg to ./#test.xvg.2#
Last frame read 1488
 
Statistics over 14881 steps [ 0.0000 thru 29.7600 ps ], 6 data sets
 
Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
-------------------------------------------------------------------------------
G96Bond                     218.248    21.5747    21.4606   0.257863    7.67451
Proper Dih.                 197.607    18.9528    18.8355   0.245025    7.29244
Improper Dih.               97.4496    13.6836    13.6688  0.0741705    2.20746
Coul-SR:Protein-Protein    -482.492    40.6716    39.0907    1.30703    38.8997
LJ:Protein-Protein         -488.321    15.9284    14.8771  -0.662376   -19.7136
Coul-LR:Protein-Protein           0          0          0          0          0
Total                      -457.507         --         --         --         --


I thank you very much for your help.

Best regards,

Pascal




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Pascal Baillod (PhD student) 
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Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
CH-1015 Lausanne	
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