[gmx-users] Inconsistency in units of virtual sites?

Douwe Pollmann douwepollmann at gmail.com
Mon Nov 20 15:50:27 CET 2017

Dear all,

I am doing simulations with a coarse grained model and I am using virtual
sites to define the positions of the side chains (SC) and the positions of
O and H atoms (HB) to include hydrogen bonding in the system.
For SC I use the 3fd option and for the HB atoms I use option 3out.
The 3fd option is specified by:
[ virtual_sites3 ]
; Site  from   funct  a    d
  n     i j k  2      0.5  -0.1

and the 3out option is given by

[ virtual_sites3 ]
; Site   from    funct  a     b     c
  n      i j k   4      1/3   0     1

3fd makes a virtual site in the same plane as the backbone atoms (*i*, *j*
and *k*) and 3out creates a virtual site pointing perpendicular to the
plane made by *i*, *j* and *k*, in this case along the bond between *i* and
For the exact details about virtual sites, see section 4.7 and 5.2.2 in the
manual: http://manual.gromacs.org/documentation/5.1.4/manual-5.1.4.pdf .

For both options you have to specify a distance from site *n* to the
backbone (*d* and *c *respectively).
However, in the case I want to have the distance SC-backbone the same as
HB-backbone, the value for *c* needs needs to be 10 times bigger than *d*.
So it seems to me I have to give the value for *d* in nm and the value for
*c* in Angstrom.

In the manual I cannot find anything about the units needed for the virtual
So my question is:
Does anyone of you know if the units for the distances in different options
for virtual sites should be the same or that they are inconsistent with
each other?

Kind regards,
Douwe Pollmann

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