[gmx-users] Inconsistency in units of virtual sites?
Douwe Pollmann
douwepollmann at gmail.com
Tue Nov 21 12:09:17 CET 2017
Ah, thank you very much, I completely missed that table..
And it is also a 'logical' unit, now I have taken a better look at equation
4.139
2017-11-21 11:23 GMT+01:00 Peter Kroon <p.c.kroon at rug.nl>:
> Hoi Douwe,
>
>
> according to the manual the units are indeed inconsistent (but
> documented, and therefore ok). See table 5.5 of the manual. For 3out the
> unit of c is in nm^-1.
>
>
> Peter
>
>
> On 21-11-17 10:15, Douwe Pollmann wrote:
> > 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?
> >
> > Kind regards,
> > Douwe
> >
> >
> >
> > 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*
> >>> 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
> >>
> >> --
> >> ==================================================
> >>
> >> 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
> >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >>
> >> ==================================================
> >>
> >> --
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