Hi,
Amber7 allows for correct treatment of extra points as massless particles,
therefore I would recommend using Amber7 and not Amber6. The mass of the
extra point (EP) will still be listed as 3, but it is treated correctly in
Amber7 MD simulations. When running the MD simulation, a smaller timestep
must be utilized, esp. in cases where the system is far from equilibrated.
You will see that such things as the density are computed corresponding to
an EP mass of 0, not 3 in Amber7.
-Sarah
On Mon, 16 Feb 2004, Nikolai Smolin wrote:
> 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
