[gmx-users] 1/viscosity from g_energy

[Justin A. Lemkul]

shikha nangia wrote:
> Dear gmx-users,
> 
> I am trying to obtain 1/viscosity values for my system after using the 
> cos_acceleration option in the mdp file. My gromacs version is 4.5.4 
> released on March 21, 2011. 
> 
> When I try using the g_energy option for my file
> 
> g_energy -f ener.edr -o outfile.xvg
> 
> I get the following options
> 
> End your selection with an empty line or a zero.
> -------------------------------------------------------------------
>   1  Bond             2  Angle            3  Improper-Dih.    4  
> LJ-(SR)      
>   5  Disper.-corr.    6  Coulomb-(SR)     7  Potential        8  
> Kinetic-En.  
>   9  Total-Energy    10  Conserved-En.   11  Temperature     12  
> Pres.-DC     
>  13  Pressure        14  Box-XX          15  Box-YY          16  
> Box-ZZ       
>  17  Box-YX          18  Box-ZX          19  Box-ZY          20  
> Volume       
>  21  Density         22  pV              23  Enthalpy        24  
> Vir-XX       
>  25  Vir-XY          26  Vir-XZ          27  Vir-YX          28  
> Vir-YY       
>  29  Vir-YZ          30  Vir-ZX          31  Vir-ZY          32  
> Vir-ZZ       
>  33  Pres-XX         34  Pres-XY         35  Pres-XZ         36  
> Pres-YX      
>  37  Pres-YY         38  Pres-YZ         39  Pres-ZX         40  
> Pres-ZY      
>  41  Pres-ZZ         42  #Surf*SurfTen   43  Mu-X            44  
> Mu-Y         
>  45  Mu-Z            46  T-System        47  Lamb-System  
> 
> 
> I am not sure which option (1 to 47) gives 1/viscosity. I tried looking 
> through the manual and searching the user list but could not resolve the 
> issue.
> 
> Please let me know what am I missing here.
> 

Use -vis rather than -o.

-Justin

> Thanks,
> SN
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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