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)
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 .