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

[Justin A. Lemkul]

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.Kass at 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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