[gmx-users] maintained an Hbond using a distance restraint
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 14 03:41:25 CEST 2011
Itamar Kass wrote:
> 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.
> All the best,
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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