[gmx-users] 1/viscosity from g_energy

[Justin A. Lemkul]

shikha nangia wrote:
> 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)
> /
> 
> 

If the proper output options are not there, then there may have been a problem 
in the .mdp file that prevented the correct energy terms from being written.  If 
present in the .edr file, it should be shown in the list (sorry, I was thinking 
of something else).  Please post your .mdp file.

-Justin

> 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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-- 
========================================

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

========================================