[gmx-users] TPI calculation in desired coordinates

Kim Q Hwan kim.qhwan at gmail.com
Wed Oct 8 03:49:21 CEST 2014

Dear all,  

I have simulate confined water between two solid crystals with infinite XY-periodic dimension. Now I want to calculate the chemical potential of the Neon atom in confined water. I think integrator=tpi option is not appropriate due to the two solids, so I am using integrator=tpic option.

I have questions.

1. Is integrator=tpic option appropriate option?
2. GROMACS manual says: "The molecule to be inserted should be centered at 0,0,0”
 Following this manual, should I center the location of the cavity where Neon atom will be inserted to 0, 0, 0? What will happen if the location of the cavity is not 0, 0, 0?
3. tpic reads the cavity location from the trajectory. But my simulation result surely doesn’t contains Neon atom. Is there any script or g_ utility including coordinate of the Neon atom to the .trr file?

Thank you.
Kim Q Hwan
Center of Nano-Liquid
Department of Physics & Astronomy
Seoul National University
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