Sorry for not attaching the datafile. I am attaching it with this post and
also pasting it at the bottom of my message.
Also my structure is just a sequence of connected glucose molecules in
vacuum. Can you please suggest how that changes the system?
isn't this obvious? you have many polar groups, many of which can form
hydrogen bonds. by changing the structure, your molecule releases
most polar molecules assume quite different conformations in vacuo
compared to being solvated in polar liquids like water or in their
crystals, where they can form interactions with neighboring molecules.
DO I change the
boundary conditions? I am also attaching an image and pdb file of the
cellulose molecule (3 unit glucose) I built.
Thank you so much for the help.
please talk to your adviser or find a competent (local) collaborator
that is willing to introduce you to the many practical details
required to understand when doing MD simulations, including issues
with calculations in vacuum. a mailing list is a poor and highly
inefficient substitute for a proper introduction into the field.
what is the proper way to proceed depends strongly on what you want to
learn from the simulations and thus is rather a question of your
research than a question of changing flags in the input.