Thankyou for such an early reply and sorry for incomplete description of the problem. Here I am including the script in which i am having the problem mentioned.
set n_solute 250 set n_solvent 500
set density 0.006 set box_l [expr pow($n_part/$density,1./3.)] setmd box_l $box_l $box_l $box_l setmd periodic 1 1 1 for {set i 0} { $i < 250 } {incr i} { set posx [expr $box_l*[t_random]] set posy [expr $box_l*[t_random]]
set posz [expr $box_l*[t_random]] set vx [gauss_random] set vy [gauss_random] set vz [gauss_random] part $i pos $posx $posy $posz type 0 v $vx $vy $vz q 2 mass 125 } for {set i 250} { $i < 750 } {incr i} {
set posx [expr $box_l*[t_random]] set posy [expr $box_l*[t_random]] set posz [expr $box_l*[t_random]] set vx [gauss_random] set vy [gauss_random] set vz [gauss_random] part $i pos $posx $posy $posz type 1 v $vx $vy $vz q 1 mass 1
}
setmd time_step 0.02 setmd skin 0.4 set temp 2.493 set gamma 1 thermostat langevin $temp $gamma
set sig 3.0 set eps 1.0 set cut [expr 2.5*$sig] set shift [expr 0.25*$eps] inter 0 0 lennard-jones $eps $sig $cut $shift 0
inter 1 0 lennard-jones $eps $sig $cut $shift 0 inter 1 1 lennard-jones $eps $sig $cut $shift 0 inter coulomb 2.3462 p3m tunev2 accuracy 1e-3
set inter_steps 50000 for {set cap 20} {$cap < 200} {incr cap 10} {
set temp [expr [analyze energy kinetic]/(1.5*[setmd n_part ])] puts "t=[setmd time] E=[analyze energy total] T=$temp" inter ljforcecap $cap; integrate $inter_steps } inter ljforcecap 0
set g [open "analysis.data" "w"] set n_part [expr ($n_solute + $n_solvent)] for {set i 0} { $i < 6000 } {incr i} { puts "step $i ftime=[setmd time] energy=[analyze energy total]"
puts "temp = [expr [analyze energy kinetic]/(1.5*[setmd n_part])]" integrate 1000
set f [open "config_$i" "w"] blockfile $f write tclvariable {box_l density} blockfile $f write variable box_l
blockfile $f write particles {id pos type v f q mass} blockfile $f write random set temp [expr [analyze energy kinetic]/(1.5*[setmd n_part ])] puts $f " \ { energy [analyze energy total] $temp}"
puts $g " [analyze energy kinetic] [analyze pressure total] [analyze energy total] $temp"
close $f } close $g
This script i am stopping after every 1000 configurations and then running it afterward with the input as the last configuration stored instead of random configuration..
And i am using the configurations both for the calculation of dynamic as well as static properties and hence the reproducibility of the trajectory is important.