From: Daniel Möller (
Date: Thu Apr 12 2018 - 17:46:58 CDT

Why not use to representation on the selection water: one with VDW (with smaller ‘sphere scale’) and one with DynamicBonds (smaller values here too)?




Daniel Möller



Von: [] Im Auftrag von Carlos Simmerling
Gesendet: Donnerstag, 12. April 2018 22:51
Betreff: Re: vmd-l: water molecules amber force field


I usually create 2 representations for the water - one using the atoms O and H1 and another using atoms O and H2.


On Thu, Apr 12, 2018 at 3:57 PM, Vermaas, Joshua <> wrote:

+1 for using a different representation. VDW is awesome, and usually you just don't show your waters. :)



On 2018-04-12 12:14:31-06:00 wrote:

This is a well-known artifact due to the fact that many simulation packages (but not NAMD, oddly enough) flag rigid water molecules by putting a bond between the hydrogen atoms inside the topology. I don't believe there is any automated solution to the problem other than to: 1) infer connectivity by some method other than the topology (e.g. a PDB) , 2) manually remove the bond, or 3) use a different representation.




On Thu, Apr 12, 2018 at 10:03 AM, Stefano Guglielmo <> wrote:

Dear vmd users,

I'm not sure whether this is an issue for vmd list: but I generated a hydrated system with amber force field (AmberTools16), but when visualizing the system in VMD water molecules appear as triangles, as if there were also a bond between the two hydrogen atoms.

Does anyone has an idea about the reason?



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