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

[Justin A. Lemkul]

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). When I looked into the tpr 
> file, the same atoms are numbered differently.
> 

Differently?  How?  The atoms may be indexed from zero, but this is not a problem.

> My questions are:
> 1. should I use the numbering as given in the topology file?

Distance restraints are applied to the [moleculetype] to which they are 
assigned.  The numbers should correspond to whatever you find in the topology 
for the protein.

> 2. Am I using it correctly? Should I use a force bigger then 20kJ?
> 

I don't think there is a firm answer here.  Do a short test and see if it 
worked, and adjust as necessary.

-Justin

> 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
> ============================================
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================