From: Nils Zimmermann (nils.zimmermann_at_cecam.org)
Date: Fri Mar 30 2007 - 04:29:01 CDT
Dear all!
I am an NAMD newbie and am wondering, if it is possible
(and how) to use the TIP4-P water model in NAMD.
I have checked the available user guide, tutorials, and
googled of course. But I don't find answers how to deal with
the mass less point charge of the TIP4-P model. NAMD sets
this to a low but non-zero value. Due to this my simulation
dies immediately, because of the high velocities of the
mass less point charge. I am using CHARRM parameter
type option. Is there a comparable option as in CHARMM
that you write something like:
LONEpair BISEctor DIST 0.15 ANGLE 0.0 DIHE 0.0 -
SELE ATOM SOLV * OM END SELE ATOM SOLV * OH2 END -
SELE ATOM SOLV * H1 END SELE ATOM SOLV * H2 END
to account for this offsite charge?
Only for completeness:
I am working on clathrate hydrates and want to use TIP4-P
because it was shown to yield better qualitative agreement
for the phase diagram of pure water than, for example,
SPC/E.
Thanks in advance for any help/hint/suggestion.
Best regards
Nils
-- ********************************************************* M.Sc. Nils Zimmermann CECAM (Centre Européen de Calcul Atomique et Moléculaire) 46, allée d'Italie 69007 LYON France www.cecam.org *********************************************************
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