[gmx-users] maintained an Hbond using a distance restraint
itamar.kass at monash.edu
Thu Jul 14 03:47:32 CEST 2011
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?
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
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
"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
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
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