[gmx-users] Imposing distance restraints between two
ghermitage at gmail.com
Fri Aug 15 06:45:45 CEST 2008
Hi, those aren't angstroms, theyre nm
1.128 1.138 ....
On Fri, Aug 15, 2008 at 9:16 AM, <plmallip at mail.uh.edu> wrote:
> Dear colleagues,
> I thank Justin for your suggesting me the distance
> restraints.So, if I want to impose a distance restraint for 11.28 A between
> two atoms 4811 and 4812, I would include the following lines in the topology
> ;ai aj type index type' low up1 up2 fac
> 4811 4812 1 0 1 11.28 11.38 11.48 1.0
> I am skeptical about low, up1 and up2 values. I used 11.28 as value for
> low, as this is the distance I want the the two atoms be far off. Up1 and
> up2 values, I added randomly 0.1 and 0.2 respectively to the low value. Let
> me know, if I am correct.
> Date: Thu, 14 Aug 2008 18:43:54 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Imposing distance restraints between two
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <48A4B52A.80800 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Maybe you would be more interested in a distance *restraint*? Note that
> constraints and restraints mean different things in Gromacs. The relevant
> manual section is 4.3, with a specific example of how to use distance
> on p. 61.
> plmallip at mail.uh.edu wrote:
> > Dear colleagues,
> > I want to impose simple distance constraint between the two
> > ends of the same protein with missing residues in between. As I went
> > through the manual I found I can use "constraints type 2" fixes the
> > distance without connecting atoms by a chemical bond.
> > Manual shows this example for O-H and H-H distances
> > [ settles ]
> > ; OW funct doh dhh
> > 1 1 0.1 0.16333
> > [ exclusions ]
> > 1 2 3
> > 2 1 3
> > 3 1 2
> > How can I do this for e.g. between two CA of the residues. Also, do
> > you suggest SHAKE or LINCS for this purpose? If you can give an example
> > for residues, just like the one above for water, that would be great.
> > Thanks in advance for any kind of suggestion in this regard.
> > warm regards,
> > Prema,
> > Graduate student,
> > UOH.
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