[gmx-users] Imposing distance restraints between two

plmallip at mail.uh.edu plmallip at mail.uh.edu
Fri Aug 15 01:46:31 CEST 2008

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 file.

;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 restraints 
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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