[gmx-users] maintained an Hbond using a distance restraint

[Itamar Kass]

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?

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>

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.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
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
============================================