[gmx-users] Problem with unwrap coordinates using the -pbc nojump flag

Μανώλης Σκούντζος m.skountzos at gmail.com
Wed Apr 4 10:13:20 CEST 2018

 Dear Gromacs users,

the problem I am facing is the following:

I am performing simulation in the NPT statistical ensemble using
a rectangular orthogonal cell consisting of one carbon nanotube (CNT)
surrounded by a host polymer matrix and in the center of the CNT I place a
water molecule. What I want to check is at which step the water molecule
exits the CNT. The problem is that when I am trying to export a pdb file
(from the binary *.xtc) with the unwrapped coordinates of the system in
order to measure the actual distance that the water has traveled during the
simulation (using the trjconv command and the -pbc nojump flag) I get
extremely strange results.
For example, when the water is at t = 0 at the one edge of the CNT and at t
= 10 ps travels to the other edge (the CNT length is 10nm and can be indeed
covered during that time interval since the CNT is empty and the water
finds no resistance to its diffusion) the coordinates of the water that are
printed in the *.pdb file are those of the image CNT. At that point, I have
to mention that it is extremely difficult (I would say impossible) the case
where the water can exit the CNT, enter the polymer region and diffuse, and
finally re-enter the image CNT. The first and third steps (entering and
leaving the CNT) are almost rare events (it lasts ~ 50ns each) and from my
experience, from another simulation of the diffusion of the water in the
polymer matrix in the absence of the CNT I have found that 4.8 * 4.8 nm^2
MSD are covered by water in ~ 4ns and not 10 ps which the case here.
Exactly the same problem I have faced with several other different initial
configuration. So I am pretty sure that using the -pbc nojump flag I obtain
not the correct results for the unwrapped coordinates of the water. Another
thing that needs to be mentioned is that when I repeat the same simulation,
using the same initial configuration (both positions and velocities are the
same) but I write more frequently (1ps instead of 10ps) then everything
worked perfect and I didn't observe any strange results into the pdb file.
The problem is that I cannot write so frequently my trajectory file since
its size would be ~10 gb.

I appreciate any help on that issue.

Thank you for your time and your help.

Emmanuel N. Skountzos.

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