Inconsistent shifts during trjconv

User discussions
1

GROMACS version: 2020.5
GROMACS modification: Yes/No
While treating pbc using gmx trjconv -s prod.tpr -f prod.xtc -o nopbc.xtc -pbc mol -center, gromacs throws me these warnings and so on -

There were 162 inconsistent shifts. Check your topology
There were 162 inconsistent shifts. Check your topology
There were 162 inconsistent shifts. Check your topology time 100.000
There were 162 inconsistent shifts. Check your topology
There were 162 inconsistent shifts. Check your topology time 200.000
There were 162 inconsistent shifts. Check your topology

What’s the issue in here, and how can I rectify it?

Thank you.

2

I am also getting the same message.
There were 52 inconsistent shifts. Check your topology
please let me know if you resolve it.

3

Sorry, I haven’t actually. Gromacs is throwing out same error to me.

4

What is the system? Is it some kind of infinite molecule like a CNT? The topic gets discussed very often (lots of info from the old mailing list as well as this forum, e.g. Inconsistent shifts)

5

Thank you very much for your response. My system has two graphene sheets and water molecules.

6

Hi Jalemkul,
My system has graphene sheets and water molecules. Graphene sheets as one group and water molecules as the second group. I want to calculate only water molecule pressure in X, Y, Z directions. How to calculate it?
I used **gmx traj ** command to extract force but it is not working.
I used ** gmx energy ** it gives whole system pressure.
Any help is appreciated.
Thank you very much.
Best regards,
Nagaraju

7

In this case, there is not a single solution to wrapping your molecule given its periodic, infinite nature. The warnings are not necessarily problematic but perhaps a more judicious choice of group for centering (a subset of atoms that can serve as a suitable reference) is appropriate.

8

I don’t think such a quantity makes sense. You can’t have “pressure of only water” because the interactions among water molecules depend on collisions with the graphene, which contributes to the virial.

9

Thank you very much for your information.
My system has water molecules between two graphene sheets. I would like to measure the pressure of water on graphene sheets. According to pressure, I will reduce water molecules to get desired pressure (certain range, ex: 0-200 bar) in the NVT ensemble.
Thank you very much.
Have a nice day!
Best,
Nagaraju