Reading the dump file for minimizing the potential energy of each configuration

LAMMPS LAMMPS General Discussion
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First of all, you should begin by reading the guidelines for posting decent questions.

If I understand your script correctly, the problem is in the loop variable. Try this:

variable nconf equal 100
variable conf loop 0 ${nconf}
label runloop
read_dump ../../coords-vel-pe.xyz $(v_conf*1000) x y z vx vy vz replace yes box no wrapped yes
minimize 1.0e-10 0 10000 10000 # why such a tight threshold?
write_dump all xyz coords-IS-$(v_conf:%03.0f).xyz # padding the variable conf to 3 digits.
next conf
jump SELF runloop

Execute with lmp -in in.lammps -l out.log

Edit: Following @akohlmey comment, I changed the variable ${conf} to $(v_conf*1000).

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