[gmx-users] Place water away from existing atoms

Javier Cerezo jcb1 at um.es
Thu May 17 12:52:08 CEST 2012

genbox calculates overlaps based on vdW radii as included in 
vdwradii.dat in the topology folder. Increase the vdW radii of carbons 
to avoid water to closer that you want. Other possibilities are 
patiently removing undesired waters by hand after solvation or using a 
"ad-hoc" script.


El 17/05/12 12:25, Steven Neumann escribió:
> Dear Gmx users,
> My system consists of a tube which is representated by atoms which are 
> not connected via bonds.
> genbox somehow place water molecules overlapping my tube atoms 
> resulting in bad contacts.
> Is there anyway to add water e.g. 4A away from existing index file of 
> my tube?
> Please, help.
> Steven

PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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