[gmx-users] 1/viscosity from g_energy

[shikha nangia]

Thanks for your instant reply, Justin.

Dear all,

Please correct me if I am woring here....but...reading through the user-list, I gathered that -vis option og g_energy oes not give good results and instead cos_accleration should be used from the following reference.
>@Article{Hess2002b,
>   author = 	 {B. Hess},
>   title = 	 {Determining the shear viscosity of model liquids from 
>molecular simulation},
>   journal = 	 {J. Chem. Phys.},
>   year = 	 2002,
>   volume =	 116,
>   pages =	 {209-217}
>}
I am trying to get the results of viscosity through cos_acceleration that probably are formatted as below (taken from a user-list). 

> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> 1/Viscosity                                         ( s/kg)

Thanks again,

SN

--- On Sat, 4/16/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] 1/viscosity from g_energy
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Saturday, April 16, 2011, 3:06 PM



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
> 
> 

-- ========================================

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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