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

[David van der Spoel]

huzhongqiao at gmail.com wrote:
> 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:
>  
>   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.



add an extra empty line and check the archives of the user list.

>  
> I tried in version 3.2.1 and this program give selections with 
> number such as
>    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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-- 
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://folding.bmc.uu.se
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