[gmx-users] TPI calculation in desired coordinates
Kim Q Hwan
kim.qhwan at gmail.com
Mon Oct 13 15:47:56 CEST 2014
OK, I think I get the right chemical potential.
Thank you for answer.
Kim Q Hwan
Center of Nano-Liquid
Department of Physics & Astronomy
Seoul National University
Sent with Sparrow (http://www.sparrowmailapp.com/?sig)
On 2014년 10월 9일 Thursday at 오전 2:55, João M. Damas wrote:
> 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 (mailto: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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