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.k...@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
========================================
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