[gmx-users] Inconsistency in units of virtual sites?
p.c.kroon at rug.nl
Tue Nov 21 11:30:05 CET 2017
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.
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,
> 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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