Umbrella sampling grompp.cpp error

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GROMACS version:2021.4
GROMACS modification: no
gmx grompp -f npt_umbrella.mdp -c conf449.gro -p topol.top -r conf449.gro -n index.ndx -o npt22.tpr -maxwarn 1
when i tried to run this command in umbrella sampling tutorial ,its giving the following error:
NOTE 3 [file npt_umbrella.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.

Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 56x40x104, spacing 0.118 0.110 0.116

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 4.868 nm 4.868 nm

Estimate for the relative computational load of the PME mesh part: 0.10

This run will generate roughly 13 Mb of data

There were 3 notes

There was 1 warning

Program: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2389)

Fatal error:
There was 1 error in input file(s)

I don’t know why this error is coming as the input file npt_umbrella.mdp , I downloaded from the gromacs tutorial itself, I am not able to un derstand why this error is coming,what does this error mean?
kindly help me with it .

2

Hi,

I guess the error indicates that pull-group1-pbcatom option in the mdp file should be defined differently (Molecular dynamics parameters (.mdp options) — GROMACS 2022.3 documentation). This option is relevant when you deal with relative large group.

\Alessandra

3

thank you alevilla it worked