[gmx-users] Spherical shaped box
kw_bagherzadeh at yahoo.com
Wed May 16 11:49:58 CEST 2012
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
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
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