VMD通过代码pbc wrap -centersel protein -center com -compound residue -all处理过后，仍然无法解决pbc...
采用了pbc wrap -center com -centersel "resname WATE" -all 处理周期性边界体条件发现统计的氢键...
1-4scaling 1.0 # CUT-OFFS switching on switchdist 10.0 cutoff 12.0 pairlistdist 13.5 PME yes PMEGridSpacing 1.0 PMETolerance 10e-6 PMEInterpOrder 4 wrapWater on; # wrap water to central cell wrapAll on; # wrap other molecules too wrapNearest off; # use for non-rectangular cells (wrap ...
pbc wrap -all -compound res # RMSD Calculation set outfile [open rmsd.dat w]#set nf [molinfo top get numframes]set frame0 [atomselect top "nucleic and noh" frame 0]set sel [atomselect top "nucleic and noh"]# RMSD Calculation Loop for {set i 1} {$i < $frames} {incr i} { $...
pbcbox/20-Nov-2006 14:04 - pbctools/18-Mar-2005 11:08 - pbcwrap/18-Mar-2005 11:08 - pdbbfactor/15-Sep-2004 18:25 - pickbond/12-Jul-2004 16:27 - potsel/12-Jul-2004 16:27 - potsurf/12-Jul-2004 16:27 - read_dx/12-Jul-2004 16:29 - ...