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