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

[David]

On Tue, 2005-07-26 at 22:14 -0500, Xiaoming Zhang wrote:
> Sorry, I should also include the bonded terms.  But those bondeds are
> for the whole system, aren't they?
yes, but if the rest is water there is no contribution to the bonded
energy.
> 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)    |
> > > |_____________|_______________________________________________________|
> > >
> >
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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