[gmx-users] Inconsistency in units of virtual sites?
jalemkul at vt.edu
Mon Nov 20 17:11:54 CET 2017
On 11/20/17 9:50 AM, Douwe Pollmann wrote:
> 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?
GROMACS only ever uses nm, except when doing I/O for PDB files, which
are in A. But the units are consistent for everything that GROMACS does.
You're probably getting weird behavior by trying to specify "a = 1/3"
rather than "a = 0.3333333"
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users