[gmx-users] potential energy of a peptide in explicit DMSO

[Xiaoming Zhang]

Thanks a lot, Anton.  I simply changed the energy group in .mdp file
from "System" to "Protein" and then I can see some energy terms for
the protein when using g_energy.  However, I am confused about which
energy terms I should used to calculate the potential energy for the
peptide.  I searched the gromacs achieve and noticed that some other
users had the same confusion but no clear answer had been provided. 
The following is my energy output from g_energy:

**************************************************************************************
Select the terms you want from the following list
End your selection with 0
   1=          Bond   2=         Angle   3=   Proper Dih.   4=Ryckaert-Bell.
   5= Improper Dih.   6=         LJ-14   7=    Coulomb-14   8=       LJ (SR)
   9= Disper. corr.  10=  Coulomb (SR)  11=  Coulomb (LR)  12=     Potential
  13=   Kinetic En.  14=  Total Energy  15=   Temperature  16=Pressure (bar)
  17=         Box-X  18=         Box-Y  19=         Box-Z  20=        Volume
  21=  Density (SI)  22=            pV  23=        Vir-XX  24=        Vir-XY
  25=        Vir-XZ  26=        Vir-YX  27=        Vir-YY  28=        Vir-YZ
  29=        Vir-ZX  30=        Vir-ZY  31=        Vir-ZZ  32= Pres-XX (bar)
  33= Pres-XY (bar)  34= Pres-XZ (bar)  35= Pres-YX (bar)  36= Pres-YY (bar)
  37= Pres-YZ (bar)  38= Pres-ZX (bar)  39= Pres-ZY (bar)  40= Pres-ZZ (bar)
  41= #Surf*SurfTen  42=  Pcoupl-Mu-XX  43=  Pcoupl-Mu-YY  44=  Pcoupl-Mu-ZZ
  45=          Mu-X  46=          Mu-Y  47=          Mu-Z 
48=Coul-SR:Protein-Protein
  49=LJ:Protein-Protein  50=Coul-LR:Protein-Protein 
51=Coul-14:Protein-Protein  52=LJ-14:Protein-Protein
  53=Coul-SR:Protein-rest  54=LJ:Protein-rest  55=Coul-LR:Protein-rest
 56=Coul-14:Protein-rest
  57=LJ-14:Protein-rest  58=Coul-SR:rest-rest  59=  LJ:rest-rest 
60=Coul-LR:rest-rest
  61=Coul-14:rest-rest  62=LJ-14:rest-rest  63=      T-System  64=   Lamb-System
48 
49
50
51
52
0

Back Off! I just backed up energy.xvg to ./#energy.xvg.4#
Reading frame     70 time   35.000           
Last frame read 76                               
WARNING: Incomplete frame: nr     77 time   38.000     


Statistics over 37501 steps [ 0.0000 thru 37.5000 ps ], 5 data sets

Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:Protein-Protein    -345.062    13.3941    12.7896  -0.367516   -13.7822
LJ:Protein-Protein         -33.7676    7.30473    7.02883  -0.183696   -6.88877
Coul-LR:Protein-Protein           0          0          0          0          0
Coul-14:Protein-Protein     719.375    9.16447    8.66907   0.274566    10.2965
LJ-14:Protein-Protein       71.2596    9.28124    9.27777 -0.0234419  -0.879095

gcq#225: "Everybody is Smashing Things Down" (Offspring)

****************************************************************************************

Is it correct to simply add up those five energies to get potential energy?


thanks,
xm



On 7/26/05, Anton Feenstra <feenstra at few.vu.nl> wrote:
> Xiaoming Zhang wrote:
> 
> > Dear users,
> >
> > I am running the MD simulation of a cyclic peptide in explicit DMSO.
> > It is straightforward to retrieve the potential energy of the whole
> > system (peptide + DMSO) using g_energy.  However, I didn't find a way
> > to calculate/retrieve the potential energy for the peptide only.  I
> > was wondering if any of you had the experience and knew how to deal
> > with it.
> 
> You need to define energy groups in your mdp file before you perform the
> simulation. Alternately, you can re-run your generated trajectory. See
> manual for more details.
> 
> --
> Groetjes,
> 
> Anton
> 
> * NOTE: New Phone & Fax numbers (below) *
> 
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
> |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
> |             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
> |_____________|_______________________________________________________|
>