Dear users,
I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K.
after 1ns of simulation in 300 K, the protein jumps out of the box and when I
use the command
trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump
followed by
trjconv_mpi -f new*.trr -s *.tpr -o new*.pdb -dump 1000
the box shape changes from dodecahedron to spherical. In Gromacs manual I read
;
" There are several possible shapes for space-filling unit cells. Some, as the
rhombic dodecahedron and the truncated octahedron approach a spherical shape
better than a cubic box and are therefore more economical for studying an
(approximately spherical) macromolecule in solution, since less solvent
molecules are required to fill the box given a minimum distance between
macromolecular images....... ".
Does it mean that it is ok and I can continue the simulation or I have to
increase the box size? After simulation in 200 K the protein juped out of the
box but using the same command the problem was fixed, without changing the box
shape.
Thank you in advance for the help
Sogol
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