Itamar Kass wrote:
Hi Justin,
Thanks for the quick replay. Regrading Q.1 that was my idea, just wanted
to be sure. Regarding Q.2, I think a more relevant phrase would be, how
big a force I can use without cancel the "validity' of my simulations?
I still can't say whether there is a direct answer to this, but a systematic
comparison of different conditions (no restraint, a few kJ/mol on the order of
typical H-bond strength, a constant that is somewhat larger, etc) can be useful
for interpretation. A restraint like this is a bias in the simulation; what you
may need to consider is whether or not the bias is so large that it could never
represent reality.
In addition, just to make it clear for myself, when I use 2 for type',
is this mean there is no time averaging? If so, is there any meaning for
disre_tau>
That's my understanding, per the documentation.
-Justin
Cheers,
Itamar
On 14/07/11 11:41 AM, Justin A. Lemkul wrote:
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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