# [gmx-users] potential energy

Michal Kolinski mkolin at iimcb.gov.pl
Wed Apr 20 17:40:42 CEST 2005

```Hi all.
I did 2ns MD  of system involving TM-protein + ligand + lipids + SOL + ions.
How can I  calculate potential energy separately for protein and separately  for ligand?

I used PME during my simulation.
My energy groups are:  protein, Mol,  DPPC, Na, SOL
G_energy gives potential energy of whole system, so in order to get potential
energy for separate molecule I need to add up all the necessary terms? (from g_energy
output).   How can I calculate LR Coulomb energies for each of the defined groups?
Is there any easy way to get potential energy for defined group?

1=          Bond   2=         Angle   3=   Proper Dih.   4=Ryckaert-Bell.
5= Improper Dih.   6=         LJ-14   7=    Coulomb-14   8=       LJ (SR)
9=  Coulomb (SR)  10=  Coulomb (LR)  11=     Potential  12=   Kinetic En.
13=  Total Energy  14=   Temperature  15=Pressure (bar)  16=         Box-X
17=         Box-Y  18=         Box-Z  19=        Volume  20=  Density (SI)
21=            pV  22=        Vir-XX  23=        Vir-XY  24=        Vir-XZ
25=        Vir-YX  26=        Vir-YY  27=        Vir-YZ  28=        Vir-ZX
29=        Vir-ZY  30=        Vir-ZZ  31= Pres-XX (bar)  32= Pres-XY (bar)
33= Pres-XZ (bar)  34= Pres-YX (bar)  35= Pres-YY (bar)  36= Pres-YZ (bar)
37= Pres-ZX (bar)  38= Pres-ZY (bar)  39= Pres-ZZ (bar)  40= #Surf*SurfTen
41=  Pcoupl-Mu-XX  42=  Pcoupl-Mu-YY  43=  Pcoupl-Mu-ZZ  44=          Mu-X
45=          Mu-Y  46=          Mu-Z  47=Coul-SR:DPPC-DPPC  48=  LJ:DPPC-DPPC
49=Coul-LR:DPPC-DPPC  50=Coul-14:DPPC-DPPC  51=LJ-14:DPPC-DPPC  52=Coul-SR:DPPC-Protein
53=LJ:DPPC-Protein  54=Coul-LR:DPPC-Protein  55=Coul-14:DPPC-Protein  56=LJ-14:DPPC-Protein
57=Coul-SR:DPPC-SOL  58=   LJ:DPPC-SOL  59=Coul-LR:DPPC-SOL  60=Coul-14:DPPC-SOL
61=LJ-14:DPPC-SOL  62=Coul-SR:DPPC-MOL  63=   LJ:DPPC-MOL  64=Coul-LR:DPPC-MOL
65=Coul-14:DPPC-MOL  66=LJ-14:DPPC-MOL  67=Coul-SR:DPPC-Cl  68=    LJ:DPPC-Cl
69=Coul-LR:DPPC-Cl  70=Coul-14:DPPC-Cl  71= LJ-14:DPPC-Cl  72=Coul-SR:Protein-Protein
73=LJ:Protein-Protein  74=Coul-LR:Protein-Protein  75=Coul-14:Protein-Protein  76=LJ-14:Protein-Protein
77=Coul-SR:Protein-SOL  78=LJ:Protein-SOL  79=Coul-LR:Protein-SOL  80=Coul-14:Protein-SOL
81=LJ-14:Protein-SOL  82=Coul-SR:Protein-MOL  83=LJ:Protein-MOL  84=Coul-LR:Protein-MOL
85=Coul-14:Protein-MOL  86=LJ-14:Protein-MOL  87=Coul-SR:Protein-Cl  88= LJ:Protein-Cl
89=Coul-LR:Protein-Cl  90=Coul-14:Protein-Cl  91=LJ-14:Protein-Cl  92=Coul-SR:SOL-SOL
93=    LJ:SOL-SOL  94=Coul-LR:SOL-SOL  95=Coul-14:SOL-SOL  96= LJ-14:SOL-SOL
97=Coul-SR:SOL-MOL  98=    LJ:SOL-MOL  99=Coul-LR:SOL-MOL 100=Coul-14:SOL-MOL
101= LJ-14:SOL-MOL 102=Coul-SR:SOL-Cl 103=     LJ:SOL-Cl 104=Coul-LR:SOL-Cl
105=Coul-14:SOL-Cl 106=  LJ-14:SOL-Cl 107=Coul-SR:MOL-MOL 108=    LJ:MOL-MOL
109=Coul-LR:MOL-MOL 110=Coul-14:MOL-MOL 111= LJ-14:MOL-MOL 112=Coul-SR:MOL-Cl
113=     LJ:MOL-Cl 114=Coul-LR:MOL-Cl 115=Coul-14:MOL-Cl 116=  LJ-14:MOL-Cl
117= Coul-SR:Cl-Cl 118=      LJ:Cl-Cl 119= Coul-LR:Cl-Cl 120= Coul-14:Cl-Cl
121=   LJ-14:Cl-Cl 122=        T-DPPC 123=     T-Protein 124=         T-SOL
125=         T-MOL 126=          T-Cl 127=     Lamb-DPPC 128=  Lamb-Protein
129=      Lamb-SOL 130=      Lamb-MOL 131=       Lamb-Cl

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050420/1dbb230d/attachment.html>
```