vitroid/GenIce

tip4p/ice

Opened this issue · 3 comments

Bnn6 commented

if I want the structure to satisfy the tip4p/ice force field,what kind of command should I use?

rusl2019 commented

To make a 3x3x3 units of a ice Ih (1h) of TIP4P/Ice water in GROMACS .gro format:

genice2 1h --water ice --rep 3 3 3 > 1h.gro
Bnn6 commented

Ok thanks. I originally wrote in this form, but when I converted the gro file to a data file with Ovito, I found that the mass of the virtual atom is 1, when in fact the mass of the virtual atom in tip4p/ice should be close to 0. It should be a problem that Ovito is not precise enough in the conversion.

vitroid commented

Thank you for your report, but as far as I understand, the mass of the virtual site of TIP4P/Ice is correctly set to zero in the recent versions of GenIce2.

Here is a short code to calculate the center of mass of a TIP4P/Ice molecule:

import numpy as np
import genice2.molecules.ice
water = genice2.molecules.ice.Molecule()
# calculate the center of mass
print(np.array([16, 1, 1, 0]) @ water.sites_)

The result is [0. 0. 0.].