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 th
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
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, du
Sorry I should mention it at the very beginning that I have a linear
molecule and the angle is to be constrained at 180 degree. So what is
the best way of constraining the angle for the linear molecule ?
On Tue, Jul 24, 2012 at 2:06 PM, Mark Abraham wrote:
> On 24/07/2012 6:07 PM, Broadbent, Ric
On 24/07/2012 6:07 PM, Broadbent, Richard wrote:
An Angle constraint amounts to fixing a triangle. To do this you need to
constrain the distances between all the atoms as you know the of the bonds
6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
trivial geometry problem calcu
An Angle constraint amounts to fixing a triangle. To do this you need to
constrain the distances between all the atoms as you know the of the bonds
6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
trivial geometry problem calculate the length of the third side of the
triangle (
Oh ! Thnaks
I saw that table, the angle_restrain option is there but not constraints .
Anyway if suppose, I fix the distance between the two terminal atoms
of the molecule, the angle will eventually be fixed at a particular
given value. Is that the logic ?
Actually I searched for this problem so ma
On 24/07/2012 3:21 PM, tarak karmakar wrote:
Dear All,
I am constraining one angle in my protein sample by incorporating " [
constraints ]" block in topology file as
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
while doing that its showing the fo
Dear All,
I am constraining one angle in my protein sample by incorporating " [
constraints ]" block in topology file as
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
while doing that its showing the following error
Program grompp, VERSION 4.5.5
Sou
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