[交流] Lammps trajectory----use VMD to make molecules whole again 已有1人参与

set mol [molinfo top]
set ring [atomselect $mol {type 3}]
set nf [molinfo $mol get numframes]
set sel [ atomselect top all ]
for {set i 0} {$i < $nf} {incr i} {
make_whole $mol $ring $i 8
}
proc make_whole {mol sel frame num} {
molinfo $mol set frame $frame
$sel frame $frame
set allcoord [$sel get {x y z}]
set num1 [expr {$num - 1}]
set boxhalf [vecscale 0.5 [molinfo $mol get {a b c}]]
set newcoord {}
while {[llength $allcoord] > 0} {
set coord [lrange $allcoord 0 $num1]
set allcoord [lrange $allcoord $num end]
set ref [lindex $coord 0]
lappend newcoord $ref
foreach atom [lrange $coord 1 end] {
set newatom {}
set dist [vecsub $atom $ref]
foreach d $dist b $boxhalf r $atom {
if {$d < -$b} { set r [expr {$r + 2.0*$b}]}
if {$d > $b} { set r [expr {$r - 2.0*$b}]}
lappend newatom $r }
lappend newcoord $newatom
} }
$sel set {x y z} $newcoord
)

Originally posted by xk6891 at 2011-07-01 14:40:56:
可以提供一下lammps trajectory的格式么，如果能和配合脚本帮着疏通一下就更感激不尽了，脚本中还有一些地方不明白

Originally posted by xiaowu759 at 2011-07-01 14:17:42:
thanks a lot for sharing this