From: Axel Kohlmeyer (
Date: Mon Oct 07 2013 - 10:25:03 CDT

On Mon, Oct 7, 2013 at 4:37 PM, John Stone <> wrote:
> Hi,
> If you see the extra bonds on your waters, and you loaded the PSF into
> VMD, it is because the bond is explicitly listed in the PSF file.
> If I'm not mistaken, this is likely related to the particular water
> model you are likely using, and it's "normal" for that water model.

it is not so much the water model itself, but the fact that CHARMM and
AMBER implement SHAKE to keep water molecules rigid through 3 bond
constraints instead of two bond constraint and one angle constraint.

its been discussed on this list many times and you can easily "clean"
your visualization with a little bit of VMD scripting like in the
attached script from a previous life of mine. ;-)


> Cheers,
> John Stone
> On Mon, Oct 07, 2013 at 04:23:19AM -0700, Ramin Ekhteiari wrote:
>> ----------------------------------------------------------------------
>> Hi dears,
>> I embedded protein into the phospholipid bilayer, and generated psf and
>> pdb file via charmm gui membrane builder, but when I try to load it into
>> VMD,
>> I see bond between the hydrogens of water molecule, as normal it should
>> not be..
>> Would be grateful for any help..
>> Cheers,
>> Ramin
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Phone: 217-244-3349

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.