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

Justin Lemkul 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
> *j*.
> 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
> sites.
> 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.
Assistant Professor
Virginia Tech Department of Biochemistry

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