If the error bar exceeds the absolute value of diffusion coefficient,
just round the number, as I exemplified below.
The error bar should correspond to the last digit of the result value,
e.g. 5 +/ -2; 0.0002 +/- 0.0001; 0.4E6 +/- 0.2E6, etc.
My immediate guess is that the problem in the code is
Yes, for some calculations the error bar values did exceed the diffusion
coefficient values.
I am using the double-precision version of gromacs. But then again the
question is whether to consider the value displayed on the terminal screen
or the one displayed in the .xvg file.
On Tue, Jul 21, 201
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
Hi,
Actually you are right. The chol.xvg file shows a value of 0.000903331 and
NOT 0.000903331*1e-5. I initially thought that the .xvg file purposely
doesn't show the "1e-5" value.
But still 0.000903331 is different from 0.0007417 which is displayed on the
terminal screen.
On Tue, Jul 21, 2015 a
Yeah.
Generally, what my observation says that in xvg file you have the round up
value which has 4 decimal digits.
But for your one it has 10 decimal degits.
Can you please try with a higher version- 4.6.x?
On Tue, Jul 21, 2015 at 10:44 AM, Ganesh Shahane
wrote:
> Hi!
>
> I am using gromacs ve
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
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 wrote:
> which version fo you use?
>
>
>
>
>
> On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane
which version fo you use?
On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane
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 c
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 80 -n index.ndx -mol
