[gmx-users] RE: diffusion constant level off

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- Expected values are estimated. For example İf the structure is reach to
converge at last 100 ns ( all simulation time is 200 ns), then in theory,
diffusion coefficients will dont change at last 100 ns.
-I have only one diffusion coefficient for each 10 ns. I have 20 diffusion
coefficients during all simulation time.
-I controlled all msd.xvg. They are linear. The plot I sent is diffusion
versus time. (Please see it again). It isnt msd vs time
- I tried to increase sampling. The results are same approximately.
Commands for trestart to 1000 ps:
Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd1.xvg
-trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 10000
# D[   Protein] = 0.1091 (+/- 0.0212) (1e-5 cm^2/s)=13.line from msd.xvg
Command for 2.diffusion:g_msd -f traj.xtc -s topol.top -o msd2.xvg
-trestart 1000 -beginfit -1 -endfit -1 -b 10000 -e 20000
# D[   Protein] = 0.0679(+/- 0.0013) (1e-5 cm^2/s)
Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd3.xvg
-trestart 1000 -beginfit -1 -endfit -1 -b 20000 -e 30000
...
Command for 3.diffusion:g_msd -f traj.xtc -s topol.top -o msd20.xvg
-trestart 1000 -beginfit -1 -endfit -1 -b 190000 -e 200000
2013/3/29 Justin Lemkul <jalemkul at vt.edu>

>
>
> On 3/28/13 7:56 PM, Dr. Vitaly Chaban wrote:
>
>> The simplest advice is to increase sampling.
>>
>>
> I think the OP needs to describe what the system is in greater detail.
>  For a simple liquid, I would opine that 200 ns is normally vast overkill.
>  For a membrane, it may not be enough.  There's just no way to say.
>
> -Justin
>
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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