Hallo Amber users,
I used Amber 6,0:
And i want to simulate TIP4P water model.
I just prepeaed in same way what descreibed for Amber 7,0.
I used next file for preparation starting configuration:
#clearVariables
Verbosity 2
addAtomTypes {
{ "EP" "Lp" "sp3" }
}
loadOff solvents.lib
aa = loadAmberParams frcmod.tip4p
savepdb TIP4PBOX tip4pbox.pdb
saveAmberParm TIP4PBOX tip4p512.parm tip4p512.crd
exit
frcmod.tip4p:
This is the additional/replacement parameter set for TIP4P
MASS
OW 16.0
EP 3.0
BOND
OW-EP 553.000 0.150
ANGLE
HW-OW-EP 0.0 120.0
DIHE
X -HW-OW-X 2 0.0 0.0 1.0
NONBON
OW 1.7699 0.1550
EP 0.0 0.0
and solvents.lib I took from amber7.ffparms.tar.gz
next file described way for preparation of TIP4P
And if I understood exactly TIP4P rigid model but in this case
dummy atom with charge possible to move and alos has a mass.
in this case mass of water molecule 16+3+1+1 = 21
it is a little of bit strange.
I startted simulation witn this files with ntc = 2
but system veeery unstable
May be I am wrong
please help me.
Thanks in adbvance
#clearVariables
logFile tip4p.log
#
# load water models
#
addAtomTypes {
{ "HW" "H" "sp3" }
{ "OW" "O" "sp3" }
{ "EP" "H" "sp3" }
}
#
# TIP4P water
#
aa = loadAmberParams frcmod.tip4p
h1 = createAtom H1 HW 0.52
h2 = createAtom H2 HW 0.52
o = createAtom O OW 0.0
ep = createAtom EPW EP -1.04
set h1 element H
set h2 element H
set o element O
set ep element H
r = createResidue T4P
add r o
add r h1
add r h2
add r ep
bond h1 o
bond h2 o
bond h1 h2
bond ep o
TP4 = createUnit TP4
add TP4 r
set TP4.1 restype solvent
set TP4.1 imagingAtom TP4.1.O
zMatrix TP4 {
{ O H1 0.9572 }
{ H2 O H1 0.9572 104.52 }
{ EPW O H1 H2 0.15 52.26 0.0 }
}
saveOff TP4 tip4p.lib
quit
--
Dipl.-Phys. Nikolai Smolin
Physikalische Chemie I
Universitaet Dortmund
Otto-Hahn-Str. 6
44221 Dortmund
Germany
Tel: +49 / 231 / 755 3929
Fax: +49 / 231 / 755 3901
E-mail: smolin.pci.chemie.uni-dortmund.de
E-mail: nikolai.smolin.uni-dortmund.de
www: http://pci.chemie.uni-dortmund.de/~smolin/
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Received on Mon Feb 16 2004 - 17:53:00 PST
