# [gmx-users] CO2 Linear triatomic - topology problem

Eudes Fileti fileti at ufabc.edu.br
Sat Jan 24 16:16:50 CET 2009

```Hi gmx-users, I am trying to build a CO2 topology.
Because CO2 is a triatomic linear molecule there
is a discontinuity in the potential for the angle of
180 degrees, so I must use virtual sites to circumvent
the problem. I have create my topology (gave below)
from arguments I read in the forum
(http://www.gromacs.org/pipermail/gmx-users/2003-February/004394.html)
and for which I was a brief summary, also below.
But when I run the simulation I get the following error message.

"virtual site D1 (Res CO2) has non-zero mass 21.90158"

I understand and agree that the message, but what
I do not understand is, why the topology for CO2 gives
this error, while that for acetonitrile (below) does not.
Someboy could help me find the error?
Thanks
eef

*** My CO2 Topology ***
[ moleculetype ]
; name  nrexcl
CO2        2

[ atoms ]
;   nr  type    resnr   residu  atom    cgnr    charge mass
1       D1       1       CO2    D1    1        0.0000  21.90158
2       D2       1       CO2    D2    1        0.0000  21.90158
3       O        1       CO2    OC    1       -0.3256   0.00000
4 C        1       CO2    CO    1        0.6512   0.00000
5       O        1       CO2    OC    1       -0.3256   0.00000

[ constraints ]
;  ai  aj funct           b0
1       2 1   0.2000

[ dummies2 ]
;  ai    aj    ak       funct   a
3     1     2       1       0.0170
4     1     2       1       0.1000
5     1     2       1 0.2170

[ exclusions ]
3       4       5
4 5 3
5 4 3

;***  ***

*** From forum ***
;For acetonitrile
;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 correct Me-N-distance from the reference i cited is 0.263nm.
;The distance R between D1(m1) and D2(m2) is in priciple free to choose.
;only if you choose it shorter than r(Me-N) the quadratic equation
;you find for the first unknown paramter to define becomes undefined:
;
;      M*R +- sqr(M^2R^2-4MIa)
;r1 = -----------------------
;               2M
;
;I got two solutions for r1. Calculating r2=r1-R will give you the
;negative of the other solution. I have chosen the solution
;that makes physical sense to me:
;
;D1--Me-------+-C--D2---N
;              ^
;              |
;             com
;You have to consider that m(D1)<<m(D2). Hence the above config makes more
;sense than the other mathematical solution:
;
;     Me-D2----+-C-------N-D1
;
;
*** ***

;*** Forum Acetonitrile Topology ***
[ 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 -------------------
*** ***

_______________________________________
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas