Sure. What's the MSD of a pendulum if you only sample at a rate equal to
the period? How often you want to sample depends on the time scale of what
you want to observe. That might be up to you to measure :-)
Mark
On Wed, May 22, 2013 at 11:41 AM, Anna Akinshina <
anna.akinsh...@manchester.ac.uk>
Hi,
For particles that diffuse more than half a box length between frames will
appear as if they haven't moved much, assuming you have periodic boundary
conditions.
Erik
On 22 May 2013, at 11:41, Anna Akinshina
wrote:
> Dear Gromacs Users,
>
> I have a question interpreting obtained msd da
Quoting afsaneh maleki :
> Hi,
>
> I am working on the simulation of protein memberane.
>
> How can I calculate MSD (mean squar displacement) of bond lipid ( as those
> phosphate atomes are written 0.35 nm of protein)?
> I know that I must use g_msd for calculating, but I need index file that
>
Hello together,
i refer here to the problem with msd mentioned at the beginning of
September (see also below): i calculate msd this time for monomers
(not for molecules as before) and i still observe finite size effects
for chains if they include fixed bonds ([constrains]), however this
effect
Hi,
g_msd calculates the msd for molecules, not for atoms.
I guess that would explain the result when you half the chain length.
It might also explain the box size effects, since whole chains will
still have a reduction in MSD due to periodiciy with a box of 3 Rg.
If you run g_msd without -mol y
Hi,
I did the calculation for water on both sides of bilayer. It is
unlikely that water molecules
donot cross the boundary. May be I need to wait for longer run such
that molecules go out of box.
I will check that. Thank you very much for your suggestions.
Regards,
Ananya.
Ananya Debnath
Ananya Debnath wrote:
Hi,
I want to calculate MSD (mean square displacement) for DPPC-WATER
bilayer system, without using g_msd tool in gromacs, but using any
other code, I
need a trajcetory which is unfolded.
From mails in mailing list I understand that people use trjconv -pbc
nojump, to
Well.
I think I agree with David 100 cations and 100 anions without
solvent (am I correct?)... probably your system is freezing and an
evidence of this is that the slope of your MSD graph tends to zero, so
your D tends to zero too.
But considering what you said about ACFs and RDFs, I thi
Roman Holomb wrote:
Dear colleagues,
Thanks for reply!
Maybe I'm doing something wrong with using g_msd .
no your system is freezing.
I have computed MD (5ns) for system containing 100 anion and 100 cation
molecules.
Results of ACFs, RDFs look good but not MSD
So I have 2_emi_BF4
Hi Roman.
Let me guess... in theory the MSD should start non-linear and after some
time become linear until the end of simulation but the g_msd output
starts linear and after become anything.
I don´t know if I´m correct about your results but this was the results
I had when trying to calcula
Hi Roman,It would help more if you mention what it does look like and why you would think it should look otherwise. Maybe you can link us an image of the graph?Haven't heard of strange behaviour concerning g_msd recently.., but haven't used it myself lately.
Cheers,TsjerkOn 4/12/06, Roman Holomb <[
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