[gmx-users] Inconsistency in units of virtual sites?
douwepollmann at gmail.com
Tue Nov 21 10:15:42 CET 2017
Thanks Justin for the reply.
I'm sorry for the inconvenience, I put 1/3 in stead of 0.3333333 in this
example for clarity, but apparently it wasn't clear at all..
Below a part of the real .itp file is shown:
; The virtual sites for the side chain beads
[ virtual_sites3 ]
;Site from funct a b
17 1 2 3 2 5.000000e-01 -0.000000
18 2 1 3 2 5.000000e-01 -0.263000
19 3 2 4 2 5.000000e-01 -0.358000
20 4 3 5 2 5.000000e-01 -0.143000
21 5 4 6 2 5.000000e-01 -0.336000
; The virtual sites for the O and H atoms to simulate hydrogen bonds
[ virtual_sites3 ]
;Site from funct a b c
33 2 1 3 4 6.6667e-01 0.0000 -1.1000
34 2 1 3 4 3.3333e-01 0.0000 1.1000
35 3 2 4 4 6.6667e-01 0.0000 1.1000
36 3 2 4 4 3.3333e-01 0.0000 -1.1000
37 4 3 5 4 6.6667e-01 0.0000 -1.1000
38 4 3 5 4 3.3333e-01 0.0000 1.1000
The distances (or actually fractions) a and b are not the problem, it is
the value for c that is problematic.
With these settings, I see in VMD what I want to see. So the distance of
site 20 to the backbone is a bit larger than the distance of the O and H
atoms to the backbone. However, when I use c = +/- 0.11 nm (which is the
most logical option because everything should be in nm as you said), the O
and H atoms are very close to the backbone, while the side chain beads are
at the correct distance.
I also checked if it is a problem that I have twice a header with [
virtual_sites3 ], but putting everything underneath one header is not the
solution to this problem..
I excluded the interactions between opposing O/H (33 34, 35 36, etc) and
also between the neighbouring O/H on both sides. So I think it cannot be
the case that those atoms are pulled together by an attractive force,
causing a factor of 10 in the distance to the bonds.
Do you or someone else have another suggestion what could go wrong?
2017-11-20 17:11 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> 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*
>> For the exact details about virtual sites, see section 4.7 and 5.2.2 in
>> 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
>> So my question is:
>> Does anyone of you know if the units for the distances in different
>> 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
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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