[gmx-users] Green Kubo viscocity calculation

[Vitaly V. Chaban]

Try 5-20fs.









On Wed, Sep 2, 2015 at 12:06 AM, Aishwary Shivgan
<aishwaryshivgan55 at gmail.com> wrote:
> Currently I saving the energies after every 50 fs. Should I decrease more?
> On Sep 2, 2015 3:23 AM, "Vitaly V. Chaban" <vvchaban at gmail.com> wrote:
>
>> 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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