[gmx-users] maintained an Hbond using a distance restraint
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 14 03:53:50 CEST 2011
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
> 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
That's my understanding, per the documentation.
> On 14/07/11 11:41 AM, Justin A. Lemkul wrote:
>> 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
>>> "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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