[gmx-users] Green Kubo viscocity calculation

[Vitaly V. Chaban]

Sure, viscosity is overestimated, since you do not save pressure
components frequently enough to account for fast autocorrelations.





On Tue, Sep 1, 2015 at 3:29 PM, Aishwary Shivgan
<aishwaryshivgan55 at gmail.com> wrote:
> Thanks,
>  Do I need any special mdp options running the simulation?
> I tried
>  g_energy -vis
> g_analyze -f visco.xvg
> it's giving me viscosities 10 times higher than actual.
>
> On Sun, Aug 30, 2015 at 2:11 AM, Vitaly V. Chaban <vvchaban at gmail.com>
> wrote:
>>
>> g_energy -vis
>> g_analyze -f visco.xvg
>>
>>
>> The method is handy only for systems with viscosity below 10 cP.
>>
>>
>>
>>
>>
>> On Sat, Aug 29, 2015 at 6:15 AM, Aishwary Shivgan
>> <aishwaryshivgan55 at gmail.com> wrote:
>> > Thank you David,
>> >              It's not there in g_energy. I am currently calculating
>> > polymer
>> > viscosity using transverse current autocorrelation function g_tcaf. I
>> > just
>> > want to compare between the tcaf and green Kubo which is widely used for
>> > polymer viscosity calculation.
>> >
>> > On Sat, Aug 29, 2015 at 2:12 PM, David van der Spoel
>> > <spoel at xray.bmc.uu.se>
>> > wrote:
>> >
>> >> On 29/08/15 10:19, Aishwary Shivgan wrote:
>> >>
>> >>> Hi gromacs users,
>> >>>           Is there way to calculate viscosity from gromacs runs using
>> >>> green
>> >>> kubo formalism?
>> >>>
>> >>> Check g_energy. How accurate these are is hard to tell, but see e.g.
>> >> Hess, J Chem Phys 116 (2002) 209-217.
>> >>
>> >> I am working on implementing more methods to compute viscosity.
>> >>
>> >> --
>> >> David van der Spoel, Ph.D., Professor of Biology
>> >> Dept. of Cell & Molec. Biol., Uppsala University.
>> >> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> >> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> >> --
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