[gmx-users] Spherical shaped box

Kowsar Bagherzadeh kw_bagherzadeh at yahoo.com
Wed May 16 11:49:58 CEST 2012

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120516/4d3959dd/attachment.html>

More information about the gromacs.org_gmx-users mailing list