[gmx-users] Test particle insertion for all atom force field

João M. Damas jmdamas at itqb.unl.pt
Sat Apr 8 16:54:09 CEST 2017


You can put the entire molecule the the end of .gro file, it shall work.
Remember that the molecule should be centered at 0, 0, 0.


On Thu, Apr 6, 2017 at 1:06 PM, Badmos, Sakiru <sakiru.badmos.14 at ucl.ac.uk>

> Hi everyone,
>                   I want to calculate excess chemical potential for some
> molecules in water. I found a tutorial on this but it was on methane
> (united atom). The insertion of the test particle requires that it is
> included as the last atom in the .gro file with coordinate 0.000 0.000
> 0.000. This works for United atom. How do I do this for molecule like CO2
> with three atoms?
>              Thank you as you help.
> Sakiru.
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

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