Dear Gromacs Users,
I have a question interpreting obtained msd data.
I need to calculate diffusion coefficient for a single argon atom in a box of
water (500 molecules).
During the calculations (50ns) I write both trr and xtc trajectories, but to
save space I write trr for whole system very
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 anna.akinsh...@manchester.ac.uk
wrote:
Dear Gromacs Users,
I have a question
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,
I was just wondering how MSDs in Gromacs are normalized. I am calculatiing MSDs
for my lipid system of different timesteps of simulation and I get much higher
results for centre of mass calculations in comparison to mass-weighted one.
And I thought about normalization issue, but I
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
is included phosphate atoms within 0.35
Quoting afsaneh maleki maleki.afsa...@gmail.com:
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
Hello,
Does anyone have additional details about how the calculations are done for
the -mol flag of g_msd when using -rmcomm? I am comparing results with and
without the -mol flag. I presume that when -mol is used the file specified
by the -o flag contains the average msd of the centers of mass
15:22:40 +0200
Subject: [gmx-users] msd
Hello together,
i have a problem with msd. i simulate a melt of chain molecules
consisting of 116 united atoms per chain. then i copy the box n
times in x,y,z directions, repeat simulations and get a slightly
different msd curves
Hi,
I am running simulations of gaseous molecules (CH4, C2H6, CO2, N2) in
a silica pore (4nm in diameter), cell dimensions, 46 x 44 x 37. This
in an infinite pore in the z direction.
I am interested in looking at diffusion but I am a bit concerned about
the shape of my MSD curves, for a
Hello together,
i have a problem with msd. i simulate a melt of chain molecules
consisting of 116 united atoms per chain. then i copy the box n
times in x,y,z directions, repeat simulations and get a slightly
different msd curves:
in the time range between 1 ps and 10 ps it flattens out
you get the MSD per atom.
Berk
From: yel...@uni-mainz.de
To: gmx-users@gromacs.org
Date: Thu, 3 Sep 2009 15:22:40 +0200
Subject: [gmx-users] msd
Hello together,
i have a problem with msd. i simulate a melt of chain molecules
consisting of 116 united atoms per chain. then i copy the box
Using g_msd on a group of atoms results in an msd vs. time plot which is
the result of an average over all the atoms' motions. I would like to
obtain the same plot, but for an average over the center of mass motions
of a group of molecules. Using the -mol option results in a plot of the
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
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 remove pbc.
So I used pbc
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
Dear all:
I've got a DOPC/cholesterol system, and I want to get the MSD of the DOPCs
near cholesterols.
According to the literature, the overall movement of the each monolayer
should be removed prior to the MSD analysis of individual molecules, my
question is how should I do this?
Thank you in
Dear users:
1. I have a lipid bilayer of POPC with cholesterols. I'm trying to calculate
the MSD of the POPCs which is nearest to cholesterols. The nearest POPCs are
defined as those POPC whose C13 atoms to O6 atoms from cholesterol distances
are less than a certain cutoff. Is there a good way to
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
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
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