From: Ana Celia Vila Verde (A.C.AraujoVilaVerde_at_uva.nl)
Date: Wed Feb 23 2011 - 11:57:03 CST
I want to simulate TIP4P2005 water using NAMD. I had a look at the
available threads in the namd mailing list and followed the suggestions
given there: modify the topology file top_all30_* (which contains the
parameters for tip4p) to use the parameters for tip4p2005 according to
the topology tutorial given in the namd website.
The tutorial explains almost everything we need to know about the
topology file, except for the two things below:
1) the atom entries for tip4p are:
ATOM OH2 OT 0.000 ECHH 0.00000 ECHA 0.00000
ATOM OM LP -0.888 ECHH 68.49000 ECHA 371.60000
ATOM H1 HT 0.444 ECHH 0.00000 ECHA 353.00000
ATOM H2 HT 0.444 ECHH 0.00000 ECHA 353.00000
What is the meaning of the fields after the charge? How does NAMD use
them in the simulation?
2) The last line for the tip4p residue is
PATC FIRS NONE LAST NONE
What is the meaning of this line?
I've searched for information on this (just googling, checking the
CHARMM website, checking the NAMD website, checking the VMD website...)
and could find none, so I'd be very grateful if anyone could shed some
light on the matter.
-- _______________________________________________________ Ana Vila Verde Post-doctoral scholar Van 't Hoff Institute for Molecular Science University of Amsterdam Science Park 904, room C2.221 1098 XH Amsterdam The Netherlands Phone: +31-(0)20-525-5141 E-mail: A.C.AraujoVilaVerde_at_uva.nl University of Minho Physics Center Campus de Gualtar 4710-057 BRAGA Portugal E-mail: avilaverde_at_fisica.uminho.pt _______________________________________________________
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