RDF and PBC corrections

User discussions
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1

GROMACS version: 2018
GROMACS modification: No

Dear all,

I want to calculate the RDF of water molecules close to my ligand. I have recentered my protein ligand system using the following commands:

gmx trjconv -s sys.md1.tpr -f sys.md1.xtc -o sys.md1.whole.xtc -pbc whole

gmx trjconv -s sys.md1.tpr -f sys.md1.whole.xtc -o sys.md1.whole.nojump.xtc -pbc nojump

gmx trjconv -s sys.md1.tpr -f sys.md1.whole.nojump.xtc -o sys.md1.whole.nojump.mol.xtc -pbc mol

After these steps, my protein-ligand system is whole and centered but the waters have drifted away from the box and are all over the place. I was wondering if there is a better way to fix the PBC in order to obtain sensible RDF results.

Thank you very much in advance,

Sara Llopart

2

Hi,
maybe this workflow may help
https://manual.gromacs.org/current/user-guide/terminology.html?highlight=workflow
\Alessandra

3

Thank you Alessandra,

I managed to fix the PBC using the following commands:

echo 0 | gmx trjconv -s sys.md1.tpr -f sys.md1.xtc -o sys.md1.whole.xtc -pbc whole

echo 0 | gmx trjconv -s sys.md1.tpr -f sys.md1.whole.xtc -o sys.md1.whole.nojump.xtc -pbc nojump

echo 1 0 | gmx trjconv -s sys.md1.tpr -f sys.md1.whole.nojump.xtc -o sys.md1.whole.nojump.tric.xtc -pbc mol -ur tric -c

Sara

1 Like
4

This is the correct fix:

echo 0 | gmx trjconv -s sys.md1.tpr -f .sys.md1.xtc -o sys.md1.whole.xtc -pbc whole -skip 100

echo 0 | gmx trjconv -s sys.md1.tpr -f sys.md1.whole.xtc -o sys.md1.whole.nojump.xtc -pbc nojump -ur tric

echo 1  0 | gmx trjconv -s sys.md1.tpr -f sys.md1.whole.nojump.xtc -o sys.md1.whole.nojump.tric.xtc -pbc atom -ur tric -center 

echo 0 | gmx trjconv -s sys.md1.tpr -f sys.md1.whole.nojump.tric.xtc -o sys.md1.fixed.xtc -pbc whole -ur tric

Sara