AW: problem with water molecules angle in MD simulation

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jan 26 2015 - 02:43:41 CST

Hi,

 

TIP3P actually has no angle property. It has 3 bonds instead. Itís not
recommended to use TIP3P without rigidbonds cause of the missing VDW term
for the hydrogens, which will disturb the temperature representation of the
whole water molecule. I donít see the issue for me, angle remains 104.49į.

 

Can you supply a onewater.parm7 file to cross check against mine?

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Shoresh Shafei
Gesendet: Montag, 26. Januar 2015 02:06
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: problem with water molecules angle in MD simulation

 

When I perform minimization using namd for proteins solvated in water I
notice that the water angles are drastically deviated from 104.5. Have you
ever had this problem? How did you fix it? For more information, here are
the steps I take:

1. I use amber to build the topology and crd files.

2. The water model is TIP3P

3. The generated pdb files by tLeap (Amber) are perfectly fine with regards
to the water angles as well as the bond lengths; They all obey the TIP3P
model.

4. After the minimization, the average angle of water molecules is around 99
degrees.

5. If I use SHAKE or SETLLE algorithms, the water bonds remain rigid
however, the water angles still deviates drastically from 104.5.

6. As I read somewhere, one possibility is that the new versions of AMBER do
not record the water angle in the topology file and consequently it is not
read by namd. But a colleague of mine is performing DNA simulations using
CHARMM (instead of amber) force field in namd and he has the same problem
with water angles.

Please let me know if I need to provide any further information.

I appreciate your comments.

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