[gmx-users] g_msd and Diffusion Constant

[V.V.Chaban]

I have a strong belief that an error bar for such numbers exceed the
diffusion coefficient values.

Newer gromacs versions (or is it just because of a double-precision
compilation?) output more digits. I do want to hope these digits are
meaningful....

If I got this situation, I would report 10^(-8)cm^2/s.





On Tue, Jul 21, 2015 at 2:14 AM, Ganesh Shahane
<ganesh7shahane at gmail.com> wrote:
> Hi!
>
> I am using gromacs version 4.5.5. The values are different. The value
> displayed on the terminal screen is 0.0007417*1e-5 cm^2/s while the value
> displayed in the chol.xvg file is 0.000903331*1e-5 cm^2/s.
>
> As you can see, both values are quite close though the value in chol.xvg
> doesn't appear to be round up.
>
> On Tue, Jul 21, 2015 at 10:20 AM, Chandan Choudhury <iitdckc at gmail.com>
> wrote:
>>
>> Hi!!
>>
>> Are the values different? Can you show us both the values?
>> I presume both values would be same.
>> The value in the xvg file would be round up.
>>
>> Chandan
>>
>>
>> On Tue, Jul 21, 2015 at 1:33 AM, V.V.Chaban <vvchaban at gmail.com> wrote:
>>
>> > which version fo you use?
>> >
>> >
>> >
>> >
>> >
>> > On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane
>> > <ganesh7shahane at gmail.com> wrote:
>> > > Dear Gromacs Users,
>> > >
>> > > I have performed a simulation of a POPC+Cholesterol bilayer. I wish to
>> > know
>> > > the diffusion constant of a particular cholesterol molecule. Towards
>> > this,
>> > > I performed a g_msd using the command as follows-
>> > >
>> > > g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 800000 -n index.ndx
>> > -mol
>> > > chol.xvg
>> > >
>> > > where index.ndx contains a single index for the cholesterol atoms in
>> > > question. In the end, I got 2 different values of diffusion constant,
>> > with
>> > > one of them being displayed on the terminal screen and the other value
>> > > in
>> > > the chol.xvg file.
>> > >
>> > > Does anyone have any idea as to which value should be taken as the
>> > > value
>> > of
>> > > diffusion constant? Any help would be appreciated. Thank you!
>> > >
>> > > --
>> > > Best Regards,
>> > > Ganesh Shahane
>> > > --
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>>
>>
>> --
>>
>> Chandan Kumar Choudhury
>> National Chemical Laboratory, Pune
>> India
>>
>> *"All work and no play makes Jack a dull boy...”*
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>
>
>
>
> --
> Best Regards,
> Ganesh Shahane