hi, all user:
i performed the dimer simulation, and want to
realize the interaction between two peptides.
but frequently, i encountered this
kind of problem: sometimes peptides moved out of the box, and sometimes
they jumped back.
i have tried so many way to pull them back with trjconv
command, but still cause some unexpected problem.
for example, peptides break to many parts ( with -pbc whole )
or diffuse out of box gradually ( with -pbc nojump )
with -ur or -center still not the trajectory i really want. i
think maybe there are some tricks to perform.
any suggestions for me ? thanks sooooooooooo
much!
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