[gmx-users] Doubt in Distance Restraints

[Uwe Richter]

Raja,

distance retraints are described in the manual (Section 4.3.4).
The potential form is given in Figure 4.13 (Gromacs 3.3 manual).
There you can find out what low (r0), up1 (r1) and up2 (r2) mean.

I also want to remind you that the distances are given in nanometers.
Hence the allowed unpenalized distance between atoms 3724 and 4734
as you defined it would be 20.9 angstroms, which probably not what
you want.

Best regards,
Uwe

raja wrote:

>Dear all,
>      My intention is to restrict Fe(II) in active site by distance
>      restraint protocol. Fe(II) is ligated by three amino acides' polar
>      atoms respectively by (1) NE2 of HIS ,(2) NE2 of HIS (3) OD1 of
>      ASP. The following is the disres itp file I used (copied from
>      manual3.3). where I edited the atom number of
>      aminoacids(3724,2839,2872) and Fe(II) as 4734. 
>############################# disres.itp
>#############################################################################
>[ distance restraints ]
>; ai   aj    type    index    type’     low   up1   up2   fac
> 3724  4734   1        0        1        0.0  2.09  0.4   1.0
> 2839  4734   1        0        1        0.0  2.25  0.4   1.0
> 2872  4734   1        0        1        0.0  2.18  0.4   1.0
>
>########################################################################################################################
>
>I do not understand the meaning of up2 and fac so I left with 0.4  and
>1.0 as such as found in manual. 
>
>In mdp file I added the following the commands
>
>###################### full.mdp
>######################################################################################
>
>define                   = -DDISRES
>disre                    = Simple
>#######################################################################################################################
>
>I expected these modifictions will restrict but those distances are not
>restrainted....why ?
>
>Kindly explain me that wheather I need to change any other parameter .
>
>With thanks !
>B.Nataraj
>
>     
>  
>