Dear GMX users,
I am trying to replicate a molecular flow of small molecules between
two solid slabs of FCC bound atoms. The slabs are bound via LJ
interactions.The flow is created by using periodicity, where the fluid
is accelerated continuously between the two slabs. The periodic box is
created
using for this?
> https://redmine.gromacs.org/issues/1354 speculates that this code is just
> broken, has been so for years, and should be removed given that nobody
> wishes to do the work to fix it ( :-( )
> Mark
> On Tue, May 23, 2017 at 11:13 AM Kamps, M. <m.ka...@student.rug
using for this?
> https://redmine.gromacs.org/issues/1354 speculates that this code is just
> broken, has been so for years, and should be removed given that nobody
> wishes to do the work to fix it ( :-( )
> Mark
> On Tue, May 23, 2017 at 11:13 AM Kamps, M. <m.ka...@student.rug.nl>
Dear GMX users,
I have some strange behaviour which I cannot explain.
I want to accelerate atoms through my box at a certain velocity. Since
I can only adjust the acceleration, I have to trial-and-error my way
to the right accelerations.
To do this, I create a smaller 'testing' simulation,
Dear Mark,
I'm sorry for being unclear. I have rectangular box (20x5x7 nm, XYZ)
where a flow should be replicated. at Z=0 and Z=7 there are two
surfaces composed of gold atoms. In between there is a fluid. The
system is open or periodic in the X and Y directions, but limited in
the Z direction by
Dear Mark,
Thanks for your answer. I did some experiments and I think I've
located the problem.
Within my simulation there are two main components: Two surfaces and a
polymer fluid. These two surfaces are created by placing gold atoms in
a FCC lattice (lattice parameters derived from the LJ
Dear GMX users,
I am struggling with understanding my systems behaviour.
I have a semi-isotropic system where my bottom and upper plane are
composed of gold FCC plates. In between is a fluid, which during
equilibration is stationary (no acceleration). I equilibrate the
system with a Berendsen
Dear GMX users,
I am working with polymers (~20 carbon atoms) in an enclosed box. In
order to fill this box with polymers, I currently use an iteration of
multiple steps.
Currently, the polymers are created via an external code, and the
resulting polymers are linear strings of polymers, with
Dear GMX-users,
I have a question relating the acceleration of certain atoms in my system.
I am trying to simulate a flow of a liquid between two gold plates.
I've created a small, narrow and long box filled with this liquid.
In order to create the flow, a acceleration is applied to the liquid.
lues. The
y-axis remains empty.
The .xyz file is created via gmx select to select multiple residue
groups, after which I am interested in the average velocity of the
selected groups. Is it possible that the three colums represent the
average velocity in each of the three directions (XYZ?)
Mark
> O
Dear gmx-users,
I've got a small question of which I can't find the answer. I have a
simulation where I want to calculate the average velocity of certain
particles. I've created an output .xvg file via the command:
gmx traj -f input.trr -s input.tpr -n input.ndx -av output.xvg
My output, is as
(previous mail was sent prematurely, my apologies)
Dear Mark,
Again, thanks for the reply.
You said I should identify groups of molecules that are to my
interest. I'm unsure how to do this.
My .gro files show no distinction between different molecules, all of
them are built the same (rows
Dear Mark,
Again, thanks for the reply.
You said I should identify groups of molecules that are to my
interest. I'm unsure how to do this.
My .gro files show no distinction between different molecules, all of
them are built the same (rows deleted for clarification).
1EthBC1 5963 18.910
Dear Mark,
Thanks again for your reply. I'm sorry for asking these probably
stupid questions, but I'm not able to figure it out.
The objects I am interested in are small polymers, consisting of three
residue groups; Eth EthE and EthB (corresponding to both the end
groups of a polymer, and the
Dear Mark,
Thanks for your reply. Correct me if i'm wrong, but your suggestion
would be to determine the position of each atom/molecule during a
frame. This process should be repeated for each frame, which is
easiest to do with a manually written (non-GROMACS) script.
With these positions per
Dear gmx-users,
I have several simulations regarding atoms flowing between two gold
surfaces. The flow of the liquid molecules show a distinct Poiseuille
flow, which was expected.
I am now interested in extracting the velocities of these liquid
molecules (total of around 3 atoms, around 700
Dear Micholas,
Thanks for your reply and suggestions!
Your idea at point 2, how can I do this? The forces and velocities are
stored in the .edr files, while the final velocities and positions are
also stored in the output .gro file right? This means I should run a
simulation just long enough
Dear GMX users,
I am trying to simulate a flow of protein over and along a surface
structure. To do this, I have a box which is very long in its x
direction, relatively small in its y direction and its z dimension is
limited by an artificially created surface. These proteins will move
in the
Dear GMX users,
I'm experiencing difficulties with my simulation.
I have created a ionic bonded, rough surface of gold atoms (3276
atoms) in the OPLS FF, which is held together with Lennard-Jones
interactions. In the same box I've placed a C4H10 (14 atoms) molecule,
although the problem also
Mark,
Thanks again for the swift reply! Stupid of me to miss that message! I
noticed some other code that was generated as output of pdb2gmx, which
I do not fully understand. Can you maybe explain some of it?
Processing chain 1 (4 atoms, 2 residues)
Warning: Starting residue EthB1 in chain not
Dear Mark,
Thanks for your reply!
I am replicating Polyethylene, of which the [polymer.rtp] and the
[polymer.hdb] are exactly the same as described by Justin Lemkul in
this link:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html
So, my rtp entries are:
;
Dear GMX users,
I have a few questions about something I don’t fully understand. I am
trying to work with polymers, where the basics are written by Justin
Lemkul via this link:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html
This works up to the point where I
> From: "Kamps, M." <m.ka...@student.rug.nl>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Strange behaviour of added atomtype in simulation
> Message-ID:
>
Dear GMX-users,
I'm experiencing difficulty with my manually added atoms to create a
metallic surface within GROMACS. My goal is to create a surface (at this
point metallic, Al) and let it interact with a protein.
In my current situation I've only modelled the aluminium surface
(non-bonded
ctions, and connected atoms? Is
this correct?
I'm kind of stuck as to how to proceed. I'm trying to implement a surface
into gromacs. This surface is obviously inorganic and can either be
metallic or ceramic, bonded or non-bonded. Is this possible?
Mark
On 11/1/16 8:44 AM, Kamps, M. wrote:
>
Dear GMX-users,
First of all, I'm sorry if my question is a stupid one. I'm pretty new to
Gromacs and I'm trying to do my best to figure it all out.
I'm trying to work with a solid surface within Gromacs. The final goal of
my simulation is to analyse the behaviour of certain proteins on a
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