[gmx-users] maintained an Hbond using a distance restraint

[Mark Abraham]

On 14/07/2011 11:28 AM, Itamar Kass wrote:
> Hi,
>
> I wish to force my system to maintained an Hbond during a simulation. 
> In order to do so I am using a distance restraint protocol, with the 
> following parameters:
>
> In the topology file/:
>
> /[ distance_restraints ]
> ; ai     aj type index type' low up1 up2 fac
>   2786 3262 1    0     2     0.295 0.305 0.315 1.0 ;
>
> and in the run input file:
>
> ; DISTANCE RESTRAINTS
> disre               =  simple
> disre_weighting     =  equal
> disre_fc            =  20
> disre_mixed         =  yes
> disre_tau           =  10
> nstdisreout         =  1000
>
> The atoms numbering was taken from the topology file ( /268LYSH    NZ 
> 2786   3.939   7.037   5.060  0.2307 -0.0416 -0.3125/ and /320GLU    
> OE1 3262   3.872   6.806   4.875 -0.2077 -0.0055 -0.1229/ ) and is 
> based the crystal structure (for atoms and distance).

Those lines are from .gro files, not topology files. 
[distance_restraints] are specific to a [moleculetype], and must use the 
atom indices established in the [atoms] section of the [moleculetype]. 
Anything found in a .gro file is irrelevant, but might be fortuitously 
accurate.

Mark

> When I looked into the tpr file, the same atoms are numbered differently.
>
> My questions are:
> 1. should I use the numbering as given in the topology file?
> 2. Am I using it correctly? Should I use a force bigger then 20kJ?
>
> All the best,
> Itamar
>
> PS I am using GROMACS VERSION 4.0.7 in double precisin on a Linux cluster.
> -- 
>
>
> "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
>
> ===========================================
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail:Itamar.Kass at monash.edu
> ============================================

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