[gmx-users] Calculating shear viscosity of a liquid - different results from different verions of Gromacs

[Mark Abraham]

Hi,

There are some known issues fixed in 4.6 (
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x) but
since the authors of this code haven't added any test cases, AFAIK it could
have gotten broken at any time. I can't see any obvious .mdp issues. I
would encourage you to attempt to replicate the original work, and see what
that tells you.

Mark

On Fri, Dec 18, 2015 at 3:33 AM Mateusz Jasik <mateusz.jasik at pwr.edu.pl>
wrote:

> Dear Gromacs Users,
>
> I am trying to obtain the shear viscosity of an imidazolium-based ionic
> liquid by using periodic perturbation method. While recalculating some of
> mine old data, it turned out, that the results I get from the Gromacs 4.6.7
> are different from those obtained from Gromacs 4.5.5 by two orders of
> magnitude.
>
> As a test I have run a calculations using the same tpr files (created by
> the 4.5.5 verison) and two versions of gromacs. The mdp file I used is
> presented below:
>
> title               = nvT MD
> integrator          = md
> constraints         = all-bonds
> dt                  = 0.001
> nsteps              = 12000000
> nstenergy           = 100
> nstlist             = 10
> nstxout             = 0
> nstvout             = 0
> nstfout             = 0
> nstlog              = 100
> nstxtcout           = 1000
> xtcprecision        = 1000
> ns_type             = grid
> coulombtype         = PME
> rlist               = 1.0
> rcoulomb            = 1.0
> rvdw                = 1.0
> tcoupl              = nose-hoover
> tc_grps             = MENIM Tf2N
> tau_t               = 0.1 0.1
> ref_t               = 303.15 303.15
> Pcoupl              = No
> gen_vel             = no
> gen_temp            = 298
> gen_seed            = 173529
> energygrps          = MENIM Tf2N
> constraint_algorithm = LINCS
> pbc                 = xyz
> cos_acceleration        = 0.01    ; I have run simulations for five
> different values, ranging from 0.01 to 0.05
>
>
> I obtained the 1/Viscosity values using "g_energy -f edr_file -s tpr_file
> -o output.xvg".
>
> Here are the values I got from the program:
>
> cos_acceleration    1/Viscosity (4.5.5)    1/Viscosity (4.6.7)
> 0.01                                   0.0583586
> 5,91038
> 0.02                                         0.3713
> 57,4981
> 0.03                                       1.24583
> 211.699
> 0.04                                       2.73402
> 475.518
> 0.05                                       4.02399
> 807.279
>
> There have previously been numerous threads regarding the viscosity
> calculations, but I haven't found any with the problem similar to this. Are
> there any differences between the two version of program that can influence
> this value? And if so, which one should I treat as the more reliable? Or
> could this be a problem from my side (for example with the parameters used)?
>
> Thanks and regards,
> Mateusz
>
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