[gmx-users] ligand-polymer interaction in triclinic unit cell

[Dallas Warren]

1/ as long as the frame within the .tpr file or first frame within the .xtc
file fed to trjconv has the molecules/particles as shown in figure 1, then
it should maintain them as such, even if they diffuse away.  I'd recheck
what you have done there.

2/ periodic_molecules is for molecules that cross the PBC boundary,
typically those that are a single long chain that links back to itself at
the other end.
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=periodic%20molecules#mdp-periodic-molecules.
The box you are visualising doen't actually exist within the simulation, it
is an artificial construct so that you can look at it. And you can place
that box where ever you like.  What is important is the relative
positioning of the molecules to each other, and whether that is valid with
respect to what you are studying.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 8 Feb 2019 at 11:36, Wei-Ta Li <weitali.md at gmail.com> wrote:

> Hello everyone,
>
> I am trying to simulate interaction of polymer with ligand. The polymer is
> represented by infinite sheet build by propagation in 2 dimensions of
> monomer obtained from crystal structure. Since the polymer was crystallized
> in triclinic unit cell, the propagation of the sheet also appears to be
> triclinic. The topology was obtained by "gmx x2top ... -pbc". The schematic
> representation of the  structure before simulation is shown below where the
> monomer units are *, L is the ligand, \ are boundaries of the unit cell and
> water is omitted for the sake of simplicity:
>
> \                \
>  \                 \
>   \                 \
>    \                 \
>     \       L         \
>      \                  \
>       \                  \
>        \**************\
>         \**************\
>          \**************\
>
> System was simulated with typical parameters and "pbc = xyz",
> "periodic_molecules = yes" flags. After extraction of trajectory with "gmx
> trjconv -s whatever.tpr -f whatever.trr -o whatever.pdb -pbc nojump -dt
> 10", the structure looks like scheme below:
>
> \                \      **
>  \                \      *
>   \                \
>    \                 \
>     \       L        \
>      \                 \
>       \                  \
>        \  ************\
>         \ *************\
>          \**************\
>
> From Gromacs manual I understand that such representation is expected
> because regardless of the input box shape the simulation proceeds in the
> brick-shape form: "Even when simulating using a triclinic box, GROMACS
> always keeps the particles in a brick-shaped volume for efficiency, as
> illustrated in Fig. 3.1 for a 2-dimensional system". Nonetheless I have 2
> questions:
>
> 1) Why "-pbc nojump" processing does not result in the representation like
> in Scheme_1? Shouldn't it put the atoms back in the original box like
> stated in the description: "nojump checks if atoms jump across the box and
> then puts them back"? Or does it mean brick-shaped box which Gromacs uses
> for simulation? Is there other way to have representation after simulation
> as in scheme 1?
>
> 2) Second question is somewhat naive, but nonetheless. Is such skewed
> representation of the polymer sheet valid for simulation set up? In other
> words, does this "skewness" have effect on polymer-ligand interaction? In
> the brick shaped representation the left side has 3 layers, but the right
> is gradual ladder-like increase of layers from 1 to 3, and then there is a
> fragment of polymer on top of the box. Does the setting "periodic_molecules
> = yes" take care of it?
>
> Thanks in advance!
> Wei-Ta Li
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