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

[Xiaoming Zhang]

Sorry, I should also include the bonded terms.  But those bondeds are
for the whole system, aren't they?
xm

On 7/26/05, Xiaoming Zhang <smash04 at gmail.com> wrote:
> 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)    |
> > |_____________|_______________________________________________________|
> >
>