I'm modeling polymer system in Lnagevin thermostat. To start I reduced my system to just 2 particles in Langevin thermostat. When I'm visualising my results I receive something very weird. The particles just jump from point in the space to another. I tried it with different number of particles with or without interactions between them and the results are always the same( No continuous type of motion , particles just jump from one place to another). As I understand I should receive brownian type of motion instead of these random huge jumps of particles. If anyone had this kind of problem please help me.
Thank you, Mike
My code looks like this:
set name "test" set ident "_2" set vmd_wait 2
setmd box_l 30 30 30
set n_part 2 inter 2 angle 1 [expr [PI]]
inter 1 harmonic 1 1
for {set i 0} { $i < $n_part } {incr i} { set posx [expr 0] set posy [expr $i*1.5] set posz [expr 0] part $i pos $posx $posy $posz v 0 0 0
}
set sig 0.1; set cut [expr 1.12246*$sig]
set eps 1.0; set shift [expr 0] inter 0 0 lennard-jones $eps $sig $cut $shift 0
for {set i 1} { $i < $n_part-1 } {incr i} {
part $i bond 2 [expr $i-1] [expr $i+1] }
for {set i 1} { $i < $n_part } {incr i} {
part [expr $i-1] bond 1 $i }
setmd time_step 0.00001; setmd skin 0.04 set temp 0.5; set gamma 2 thermostat langevin $temp $gamma
close $vmdout_file puts "PSF and PDB written. IMD connection on port $port" puts "Start VMD in the same directory on the machine you like :"
puts "vmd -e vmdoutput.script &"