When I input the command line:
gmx grompp -f npt_umbrella.mdp -c conf207.gro -p topol.top -r conf207.gro -n index.ndx -o npt4.tpr
it will remind me:
There is an error in input file(S)
The details are as follows:
ERROR 1[file npt_umbrella.mdp]
When the maximum distance from a pull group referrence 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 pbctom. Pull group 1 is larger than that and does not have a specific atom selected as reference atom.
But the key is that I can successfully run the command
gmx grompp -f npt_umbrella.mdp -c conf6.gro -p topol.top -r conf6.gro -n index.ndx -o npt0.tpr
The npt1~3 has been created. This means some parts are OK, the others are not.
What’s more, I got file npt_umbrella.npt from GROMACS tutorial, which means it shouldn’t be wrong theoretically.
A possible cause could be that pull group 1 was being stretched when you were generating the different configurations such that by conf207, it was large enough to generate the error. Have you tried visualizing the configurations to see if this is the case?
Thank you for your help.I have visualed the configurations. I found one possible error: the pull distance is too long that the whole molecular fills all the box space. I think maybe the box size is too small.Should I change the box size for a large one?
Yes, that should be the most straightforward solution. Make sure that not only is the pull group within a quarter of the box size (to avoid the error you previously got), but also that the distance between the 2 groups being pulled is always within half the length of the box along the pulling direction. For example, if the box length is 4 nm along the direction of pulling, the pull groups must not be pulled greater than 2 nm apart, once the simulation reaches a point where the pull groups are 2 nm apart, you’ll get an error.