Mikheil Azatov wrote:
> Hi,
>
> 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 $gamma
>
>
>
> writepsf "$name$ident.psf"
> writepdb "$name$ident.pdb"
> for {set port 10000} { $port < 65000 } { incr port } {
> catch {imd connect $port} res
> if {$res == ""} break
> }
> set HOSTNAME [exec hostname]
> set vmdout_file [open "vmdoutput.script" "w"]
> puts $vmdout_file "mol load psf $name$ident.psf pdb $name$ident.pdb"
> puts $vmdout_file "rotate stop"
> puts $vmdout_file "imd connect 127.0.0.1 $port"
> puts $vmdout_file "mol modstyle 0 0 CPK 0.5000000 0.100000
> 8.000000 6.000000"
> puts $vmdout_file "mol modcolor 0 0 SegName"
>
> 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 &"
>
> exec /usr/local/vmd/bin/vmd -e vmdoutput.script &
> imd listen $vmd_wait
>
>
>
> set integ_steps 1
> for {set i 0} { $i < 50000 } { incr i} {
> set temp [expr [analyze energy kinetic]/((6/2.0)*$n_part)]
> puts "t=[setmd time] E=[analyze energy total], T=$temp"
> integrate $integ_steps
> imd positions
> }