[gmx-users] make ghost atom

ilona.baldus at bioquant.uni-heidelberg.de ilona.baldus at bioquant.uni-heidelberg.de
Wed Mar 24 09:55:04 CET 2010

I'm not sure if this helps, but have you tried link/ dummy atoms like  
you use them for QMMM? For dummies add a line to ff***nb.itp where you  
define them to have neither charge nor weight (also 0 for LJ-pot).
Then add them to your topology-file. Check out


Quoting "Park, Jae Hyun nmn" <parkj at ornl.gov>:

> Dear all,
> I would like to change a specific atom into a ghost particle (no   
> interaction with system) after some time (for example, 1ns).
> Is there any way to implement it in GROMACS?
> If I need change the code, what file do I have to look at?
> I would deeply appreciate any comments.
> Jae H. Park
> Jae Hyun Park, Ph.D.
> Physics Division
> Oak Ridge National Laboratory
> P.O. Box 2008, MS-6372
> Oak Ridge, TN 37831
> Phone (865) 241-1482
> E-mail parkj at ornl.gov

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