From: PQCHEN (namd_at_eyou.com)
Date: Wed Nov 26 2003 - 20:05:59 CST
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
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!
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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