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

[Itamar Kass]

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.

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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