How to remove water to see the molecule

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1

Dear LAMMPS mailing list;

My question relate with visualization of the simulation results done by lammps. Does anybody know how can we remove water from the simulation box during visualization, so we can easy see the molecules, for instance by VMD? We are simulating the effect of temperature on complex copolymer molecules in water and it is very difficult to see the copolymer conformation in visualization.

I’m sorry if my question is not directly related to lammps.

All the best,

Xu

2

I’m sure VMD has a way to remove water. Also you
can define a group in LAMMPS that is all your
non-water atoms and just dump those.

Steve

3

Thank you for your help. It was really useful for me.

In another case, how can I show water molecules that only are in a certain distance to the copolymer (first and second hydration layer). For example 3.5 A. What is your suggestion to achieve this?

4

There is no simple way to get LAMMPS to dump exactly those
water molecules. I suggest post-processing a dump
file to remove far-away waters. Possibly VMD has some
capability to do that during its viz procedure.

Steve

5

Thank you for your help. It was really useful for me.

In another case, how can I show water molecules that only are in a certain distance to the copolymer (first and second hydration layer). For example 3.5 A. What is your suggestion to achieve this?

VMD can do this.