i am trying to do umbrella sampling of 2 AU molecules but whenever I am trying to run the md_pull.mdp file it giving an error :
ERROR 1 [file md_pull.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.
ERROR 2 [file md_pull.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 2 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 4221 2111
2 4221 6332 0.488 nm 0.488 nm
Estimate for the relative computational load of the PME mesh part: 0.10
NOTE 3 [file md_pull.mdp]:
This run will generate roughly 5408 Mb of data
Hi,
I suggest you see the links on the topic.
https://www.vedantu.com/iit-jee/center-of-mass
http://www.physics.arizona.edu/~varnes/Teaching/141Hspring2004/Notes/Lecture16.pdf
https://www.quora.com/How-can-you-find-the-center-of-mass-of-a-water-molecule
https://study.com/learn/lesson/center-of-mass-equation-examples.html
https://www.youtube.com/watch?v=O-q-MAYpNLI
http://hyperphysics.phy-astr.gsu.edu/hbase/cm.html
https://www.omnicalculator.com/math/center-of-mass
Best regards
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