[gmx-users] setup problem

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 7 01:20:22 CET 2007

merc mertens wrote:
> hello,
> i have got a problem with my simulation setup. i prepare a protein with two ligands in a dodecahedral box. after the setup the ligands are situated in the active site of the protein all right. when i look at the structure after em one of the ligands is now outside the protein in the solvent. if i generate symmetry mates the ligand is perfectly at its typical position in the active site of the next symmetry related molecule. yet the flag "-pbc nojump" in trjconv does not produce a whole molecule!! therefore it seems that the ligand is translated during the em step. when i look at the structure before em i see that the ligand is outside the solventbox (but inside the dodecahedral box!!!) and translated inside the solventbox after em. unfortunately i have no idea how to solve this problem except to make the box so huge, that calculation becomes too time consuming, as the protein is a tetramer with nearly 1500 residues.

Have you tried the trjconv option that puts the COM of each molecule (or 
residue, I forget) inside the box?


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