[gmx-users] Artificial Shear Flow and Inconsistent Shift Error

He, Yang yang.he at mavs.uta.edu
Mon Jun 29 18:07:35 CEST 2009

Hi All,

1. Artificial Shear Flow: I am trying to do translocation studies and wanted to generate a shear flow without actual water atoms. I checked the mail list and it was mentioned that there is no velocity profile but an option to accelerate the atoms in a group. But I wanted to get the shear flow or the velocity profile without atoms.

To make myself clear: I want the boat to navigate through water, with the flow of water but there is no water, am I making sense? So I want an artificial force applied constantly in the channel not on the particle so basically I define the velocity profile using the artificial force.

2. Inconsistent Shifts Error: I received this error in my simulation studies when I used PBC =xyz " There were XXX inconsistent shifts. Check your topology ", checked the mail-list and found the option of pbc = full should be used, but seems it is not available anymore in gromacs 4.0.3, My system is very small around 1000 atoms, and it works fine without periodic conditions, but when pbc is added it runs for some time and then gives me the error.

What does this error actually mean?

How can I resolve this?



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