From: Fangqiang Zhu (fzhu_at_ks.uiuc.edu)
Date: Thu Nov 27 2003 - 23:11:33 CST
You don't need to remove that angle. Water molecules are treated specially in NAMD. When "rigidbonds" is used,
NAMD actually constraints the two O-H bonds and the H-O-H angle of a water molecule. As long as that angle
is present, NAMD will simply ignore the H-H bond of the water molecule. So you don't need to change the topology
file, and there won't be additional constraints in the simulation. Actually, if you like, you can remove the H-H bonds
of water molecules, and that won't change the result of the simulation at all.
> Dear NAMD-user,
> In the topology files, I have find the topology for the TIP3 water model.
> RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral
> 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
> ACCEPTOR OH2
> PATCHING FIRS NONE LAST NONE
> When I want to use shake to constaints the water model to rigid, do I need remove the Angle section for H1 OH2 H2?
> As we know, when when use shake to rigid this water, and we will use 4 constaints conditions. And the degrees of freedom
> will left is just 3*3-4=5, Which is incorrect since each molecule can translate and rotate. I think We will use 6 degrees of
> freedom to model the molecule translate and rotate(3 for translate and 3 for rotate). So I think we can remove the section
> of angle H1 OH2 H2 for the TIP3P water model. Is it correct.
> Any hints will be wellcome.
> Thank you in advance!
> Sincerely yours
> PeiQuan Chen
> PeiQuan Chen Department of Chemistry, Nankai University
> WeiJin Road 94, TianJin, 300071, P.R.China
> phone: (86)2223506728 Mobile Phone: (+86)13920675030
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