Thanks for the clarification.
Forgot that virtual sites have no mass. With this info it is clear why a
setup with 2 'normal' and one dummy atom would not work.
Am 26.07.2012 01:42, schrieb gmx-users-requ...@gromacs.org:
On 26/07/2012 4:12 AM, Broadbent, Richard wrote:
>Virtual sites are by d
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 oxy
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
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 ]
; Namenrexcl
CO2 2
[ atoms ]
; nr type resnr residue atom cgnr charg
As others said:
type 2 virtual site
check chapter 4.7 and 5.2.2 in the manual (version 4.5.x).
Greetings
Thomas
Am 24.07.2012 12:00, schrieb gmx-users-requ...@gromacs.org:
Sorry I should mention it at the very beginning that I have a linear
molecule and the angle is to be constrained at 180 de
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