[gmx-users] Three-site model for acetonitrile
Christoph Freudenberger
christoph.freudenberger at chemie.uni-ulm.de
Wed Feb 26 17:46:33 CET 2003
Anton Feenstra wrote:
> It seems quite OK, however it seems you simply moved mass from the
> C to the Me and N atoms (I'm not sure, since I don't know the exact
> masses of the atoms). This will influence the moments of intertia
> of your molecule (i.e. it will tumble slower).
>
> The way to do this more accurately, is to calculate the inertia tensor
> for your normal, three mass molecule, and then calculate the distance
> and masses for a two mass system with the same total mass and the same
> inertia tensors. For a linear molecule, this is quite trivial to do.
> You will find that the two masses will need to be closer together than
> your Me and N atoms are. Then, if you have the two masses at their
> appropriate distance, you construct *all* *three* atoms (Me, C and N)
> from the two dummy masses.
>
> You will now have a system of two masses that accurately reproduce
> the mass and moments of inertia of acetonitile and three 'dummy' atoms
> that accurately reproduce the normal atomic interactions of acetonitrile.
Thanks for your suggestions... yes I just moved the mass of the carbon
into the methyl and N with the condition of the com to be preserved.
setting dispcorr improved things a little bit but the densities are
still too low:
expt dispcorr=no dispcorr=enerpres
780 720 740
So maybe it's due to the error in the moment of inertia...
Just to see if I did every thing right:
The com of MeCN I get from:
M = sum(mi)
rcom = sum(mi*ri)/M
The inertia tensor of a linear molecule is:
[Ia 0 0]
I = [0 Ia 0] with Ia=sum(mi(ri-rcom)^2)
[0 0 0]
Now I have to choose to masses m1 and m2 with r1 and r2 relativ to the com:
The distance R between m1 and m2 can be chosen freely:
R = r1 - r2
There are three conditions to be satisfied:
M = m1 + m2
m1*r1 + m2*r2 = 0
m1*r1^2 + m2*r2^2 = Ia
Using these 4 eqn I can calculate the four unknows.
The new topology would come out this way:
;------------------------------------------------------
[ atomtypes ]
;type mass charge ptype c6 c12
D1 9.49031 0.000 D 0.0 0.0
D2 31.56239 0.000 D 0.0 0.0
MeAN 0.00000 0.000 A 0.90571E-02 0.26212E-04 ; (*)
CAN 0.00000 0.000 A 0.51454E-02 0.12167E-04 ; (*)
NAN 0.00000 0.000 A 0.26955E-02 0.28943E-05 ; (*)
[ moleculetype ]
; name nrexcl
Acetonitril 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 D1 1 MeCN D1AN 1 0.000 9.49031
2 D2 1 MeCN D2AN 1 0.000 31.56239
3 MeAN 1 MeCN C3AN 1 0.206 0.00000
4 CAN 1 MeCN C4AN 1 0.247 0.00000
5 NAN 1 MeCN N5AN 1 -0.453 0.00000
[ constraints ]
; ai aj funct b0
1 2 1 0.26300
[ dummies2 ]
; ai aj ak funct a
3 1 2 1 0.2652197
4 1 2 1 0.8203527
5 1 2 1 1.2652197
[ exclusions ]
3 4 5
4 5 3
5 4 3
;(*) E.Guardia, Mol. Simul. 26, 2001, 2878;
;A rigid two mass system with the same mom. of inertia
;as MeCN is used to provide a linear molecule. Me, C and
;N are defined as dummies relativ to D1 and D2.
;---------------- eof -------------------
How does that look...? I will start the new simulation
as soon as possible
regards
--
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
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