AMBER Archive (2004)

Subject: AMBER: TIP4P extended

From: Nikolai Smolin (smolin_at_steak.chemie.uni-dortmund.de)
Date: Mon Feb 16 2004 - 11:10:19 CST

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" "Lp" "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_at_pci.chemie.uni-dortmund.de
E-mail:  nikolai.smolin_at_uni-dortmund.de
www: http://pci.chemie.uni-dortmund.de/~smolin/

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu