[gmx-users] TPI calculation in desired coordinates

João M. Damas jmdamas at itqb.unl.pt
Wed Oct 8 19:55:45 CEST 2014

Hello Kim,

1. Yes, if you choose the cavity location and radius to be inside the water

2. the molecule to be inserted and cavity location are two distinct things.
The molecule to be inserted should be found on the .tpr supplied to mdrun
-rerun. The molecule should be centered at 0, 0, 0 because what the tpic
code does while "inserting" the molecule is to shift the molecule's
position to the inside the cavity you provided by summing a vector
equivalent to the cavity location you supplied (plus a random bit to give a
random location inside the cavity). If the molecule to be inserted is not
centered at 0, 0, 0, it may not be getting inserted where you want it to be
inserted. For Neon, it's trivial to make it centered at 0, 0, 0. ;-)

3. the cavity location, unlike the molecule to be inserted, is provided in
the trajectory. There isn't, up to my knowledge, any tool to do this. So
you have to manually edit the original trajectory (keep the original
though). For each frame, you'll have to insert a final line which will have
the coordinates for the cavity location. You probably will have to convert
your trajectory from binary formats to ASCII formats in order to do that
(extra tip: you can construct a script to give different cavity locations
inside the water slab for each frame).

I hope this helps.


On Wed, Oct 8, 2014 at 2:49 AM, Kim Q Hwan <kim.qhwan at gmail.com> wrote:

> 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
> Sent with Sparrow (http://www.sparrowmailapp.com/?sig)
> --
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

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