On 26/07/2012 4:12 AM, Broadbent, Richard wrote:
Virtual sites are by definition have no mass.
If you simply ignore the mass of the carbon the molecule will be too light
and its translational momentum will therefore be too small meaning it will
move too quickly.
If you place half the mass of the carbon on each oxygen the moment of
inertia will be wrong and the molecule will spin too slowly.
All correct so far.
In practice you have to decide what you want to loose or if a balance
between the two is better.
Not true, as illustrated by the link I gave earlier in the thread, which
nobody seems to have read/understood.
One needs at least two massive particles to describe the available
degrees of freedom of a linear molecule, and using exactly two
side-steps the angle constraint issue. Each must have half the total
mass of CO2 and the distance between them is chosen to reproduce the
moment of inertia. These will not be in suitable positions to have
non-bonded interactions, of course. Then three (massless) virtual sites
are constructed from those two, and these are the only ones that have
the non-bonded interactions.
Richard
On 25/07/2012 14:44, "Thomas Schlesier" <schl...@uni-mainz.de> wrote:
Ok, read the topic about the acetonitril. But i'm somewhat clueless:
Why is the following setup wrong:
Use 2 particles as normal atoms. Put the third as a dummy in between.
Give each particle its 'normal' mass?
I would assume that this system should have the right mass and moment of
inertia, due to the fact the all individual masses and the positions one
the particles would be correct.
The virtual site so constructed cannot have mass, so this cannot be an
accurate model.
Only idea i have, why this setup could be flawed, would be that the
third particle does only interact indirectly through the other two
particles (i mean, virtual site interacts normally with all othe
particles, but the force which would act on the dummy get redistributed
to the other particles)... and then it's mass does not come into play,
since it new position is determined only by the other two particles. so
the complete molecule would move with a reduced mass?!?
Still not an accurate model - you'd have a CO2 with three sites and mass
only at two of the sites, so either the mass or moment of intertia must
be wrong.
Mark
Can anyone comment on this?
greetings
thomas
On 25/07/2012 10:08 PM, Thomas Schlesier wrote:
What you have done there looks very strange...
easiest wy would be:
define the two oxygens as normal atoms (1,2), give them a bondlength
twotimes the C-O bond length
define the carbon as a dummy (3), while you construct it's position
from both oxygens with a=0.5
one thing i don't know is how to handle the mass:
1) give both oxygen half of the system mass
2) give all atoms their normal mass
would tend to (2)
One should want to get both the total mass and the moment of inertia
correct...
http://lists.gromacs.org/pipermail/gmx-users/2003-September/007095.html.
Mark
greetings
thomas
Am 25.07.2012 13:15, schrieb gmx-users-request at gromacs.org:
How to choose the positions of the dummy atoms while constraining the
angle for a linear triatomic molecule?
The topology for a such molecule ( af for example CO2 ) is as follows
[ moleculetype ]
; Name nrexcl
CO2 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 503 CO rtp CO q 0.0
1 D1 503 CO D1 1 0 21.90158
; qtot 0
2 D2 503 CO D2 2 0 21.90158
; qtot 0
3 CE 503 CO CO 3 0.7 0.00000
; qtot 0.7
4 OE 503 CO OC1 4 -0.35 0.00000
; qtot 0.35
5 OE 503 CO OC2 5 -0.35 0.00000
; qtot 0.35
[ 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
The .rtp file for CO2
[ CO ]
[ atoms ]
D1 D1 0.0000 1
D2 D2 0.0000 2
CO CE 0.7000 3
OC1 OE -0.3500 4
OC2 OE -0.3500 5
[ bonds ]
CO OC1
CO OC2
Can anyone please check above file parts whether I'm doing correct or
not ?
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