[gmx-users] (no subject)

shakira shukoor shakirashukoor1993 at gmail.com
Sat Mar 16 08:59:48 CET 2019

Dear all
I encountered with following error when running the umbrella sampling
simulation of a protein. What modification should I make in the pull code
to get rid of the error.

ERROR 1 [file npt_umbrella.mdp]:
  When the maximum distance from a pull group reference atom to other atoms
  in the group is larger than 0.5 times half the box size a centrally
  placed atom should be chosen as pbcatom. Pull group 1 is larger than that
  and does not have a specific atom selected as reference atom.

Pull group  natoms  pbc atom  distance at start  reference at t=0
       1       226       113
       2       226       339       1.396 nm          1.396 nm
Estimate for the relative computational load of the PME mesh part: 0.14
This run will generate roughly 13 Mb of data

Thanks in advance

*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
IIT Patna
Patna 801106

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