VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Wed Jul 05 2023 - 12:32:43 CDT

Hi Cindy,

Definitely okay! NAMD doesn’t need the H-H bond to make waters rigid as long as rigidBonds is set to water or all. I think other simulations programs will handle it similarly, as long as they know which molecules are water. All that being said, it’s harmless to add the bond back.

You can also remake wat.psf to add the bond and replace it in your VMD installation if you like.

Best,
JC

On Jul 5, 2023, at 2:14 AM, Cindy Cregier <cindy.cregier_at_REMOVE_yahoo.com<mailto:cindy.cregier_at_remove_yahoo.com>> wrote:

When creating a water box using VMD, would it be valid to edit the wat.top file to conform to CHARMM36 specifications?

The wat.top file sent with the updates is as follows:

27 1


MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN
MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN

RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
BOND OH2 H1 OH2 H2
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE

END
I'd like to edit the wat.top file so that the line with the H-H "bond" is uncommented, and the version is changed to 31:


31 1

MASS -1 HT 1.00800 H ! TIPS3P WATER HYDROGEN
MASS -1 OT 15.99940 O ! TIPS3P WATER OXYGEN


RESI TIP3 0.000 NOANG NODIH ! tip3p water model
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
ANGLE H1 OH2 H2 ! required
DONOR H1 OH2
DONOR H2 OH2
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE

END

Along the same vein, would the wat.psf file used by solvate.tcl work, or would a similar file need to be created using the CHARMM36 specifications for water? What specifications were used to make the wat.psf file used by VMD?

I appreciate any insight you may have!
Cindy