[gmx-developers] Problem with g_energy in Gromacs 3.3!

huzhongqiao at gmail.com huzhongqiao at gmail.com
Sat May 20 14:01:22 CEST 2006

 Dear all,
 I tried to use g_energy to calculate potential energy in Gromacs 3.3. But
surpringly, the program give the information as follows letting me to

  Select the terms you want from the following list
G96Bond                 G96Angle                Proper-Dih.
Improper-Dih.           LJ-14                   Coulomb-14
LJ-(SR)                 Coulomb-(SR)            Potential
Kinetic-En.             Total-Energy            Temperature
Pressure-(bar)          Vir-XX                  Vir-XY
Vir-XZ                  Vir-YX                  Vir-YY
Vir-YZ                  Vir-ZX                  Vir-ZY
Vir-ZZ                  Pres-XX-(bar)           Pres-XY-(bar)
Pres-XZ-(bar)           Pres-YX-(bar)           Pres-YY-(bar)
Pres-YZ-(bar)           Pres-ZX-(bar)           Pres-ZY-(bar)
Pres-ZZ-(bar)           #Surf*SurfTen           Mu-X
Mu-Y                    Mu-Z                    Coul-SR:Protein-Protein
LJ-SR:Protein-Protein   Coul-14:Protein-Protein LJ-14:Protein-Protein
Coul-SR:Protein-rest    LJ-SR:Protein-rest      Coul-14:Protein-rest
LJ-14:Protein-rest      Coul-SR:rest-rest       LJ-SR:rest-rest
Coul-14:rest-rest       LJ-14:rest-rest         T-rest

I tried to input "Potential" but failed to get results.

I tried in version 3.2.1 and this program give selections with number such
   1=      G96Angle   2=   Proper Dih.   3= Improper Dih.   4=         LJ-14
   5=    Coulomb-14   6=       LJ (SR)   7=       LJ (LR)   8=  Coulomb (SR)
   9=  Coul. recip.  10=     Potential  11=   Kinetic En.  12=  Total Energy
  13=   Temperature  14=Pressure (bar)  15=        Vir-XX  16=        Vir-XY
  17=        Vir-XZ  18=        Vir-YX  19=        Vir-YY  20=        Vir-YZ
  21=        Vir-ZX  22=        Vir-ZY  23=        Vir-ZZ  24= Pres-XX (bar)
  25= Pres-XY (bar)  26= Pres-XZ (bar)  27= Pres-YX (bar)  28= Pres-YY (bar)
  29= Pres-YZ (bar)  30= Pres-ZX (bar)  31= Pres-ZY (bar)  32= Pres-ZZ (bar)
  33= #Surf*SurfTen  34=          Mu-X  35=          Mu-Y  36=          Mu-Z
  37=      T-System  38=   Lamb-System
In this case, I can input "10 0" to calculate potential energy.

So who has used this program in Gromacs 3.3 and give me some guidance? If
you are right, it means that there is something wrong in installation of
Gromacs 3.3.1 in my cluster. Thank you very much.

Zhongqiao Hu
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