Re: [gmx-users] REMD protein-ligand separation

2009-01-07 Thread Mark Abraham
David Osguthorpe wrote: Hi, I have performed a REMD simulation of a protein and ligand in water as usual the protein and ligand get separated by symmetry operations however attempts to fix this using trjconv and the standard recipes (eg. -pbc whole, -pbc nojump) do not appear to be working i

Re: [gmx-users] REMD protein-ligand separation

2009-01-07 Thread Iakov Polyak
Dear David, Did you also use "-ur compact" in trjconv command? It must help if you use dodecahedron or octahedral geometry.. I also noticed that in 3.3.3 version one should use -pbc mol (not -pbc whole) parameter, but in 3.3.1 I'm using "-pbc whole -ur compact" in 3.3.1.. Sorry if it didn't help.

[gmx-users] REMD protein-ligand separation

2009-01-07 Thread David Osguthorpe
Hi, I have performed a REMD simulation of a protein and ligand in water as usual the protein and ligand get separated by symmetry operations however attempts to fix this using trjconv and the standard recipes (eg. -pbc whole, -pbc nojump) do not appear to be working in particular after using