[gmx-users] 1/viscosity in g_energy

[Justin A. Lemkul]

Alif M Latif wrote:
> 	
> Dear GROMACS users and developers,
> 
> I'm having trouble getting values for my 1/viscosity calculation which 
> obtained from g_energy:
> 
> g_energy -f md1_vis.edr -o md1_vis_1perv.xvg
> 
> 
> the output:
> 
> Statistics over 1000001 steps [ 0.0000 through 2000.0000 ps ], 1 data sets
> All statistics are over 100001 points
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> 1/Viscosity                       0          0          0          0  (m 
> s/kg)
> 
> gcq#310: "Shoot them in the back now" (The Ramones)
> 
>  Have I done something wrong with my simulation? If that's the case, 
> then this is my mdp parameter:
> 

This bug has been fixed in the development version of the code.  You can 
download it from the git repository:

http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Stable_version

-Justin

> cpp             = /lib/cpp
> include          = -I../top
> integrator         = md
> dt             = 0.002
> nsteps           = 10000
> nstxout          = 100
> nstvout          = 100
> nstlog           = 1000
> nstenergy         = 100
> nstxtcout         = 100
> xtc_grps         = System   
> energygrps         = System 
> nstlist          = 10
> ns_type          = grid
> 
> rlist             = 1.0
> 
> ; PME chosen as the best option to calculate viscosity ;
> coulombtype         = PME
> rcoulomb         = 1.0
> 
> rvdw             = 1.4
> 
> pbc                      = xyz
> 
> tcoupl           = berendsen
> tc-grps          = System  
> tau_t             = 0.1
> 
> ; temperature supposed to set to 20*C @ 293.15 K as reference work ;
> ref_t             = 293.15
> 
> Pcoupl           = no
> 
> gen_vel          = yes
> gen_temp         = 298.15
> gen_seed         = 173529
> 
> constraints         = none
> 
> 
> ; NEMD ;
> 
> acc_grps                  = system
> accelerate                = 0.1 0.0 0.0
> cos_acceleration          = 0.02
> 
> 
> Any suggestion are most welcomed and thank you in advance!
> 
> 
> 
> MUHAMMAD ALIF MOHAMMAD LATIF
> Laboratory of Theoretical and Computational Chemistry
> Department of Chemistry
> Faculty of Science
> Universiti Putra Malaysia
> 43400 UPM Serdang, Selangor
> MALAYSIA
> 
> 	
> 
> 	
> 
> 

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

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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