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

[Itamar Kass]

Thanks!

Itamar.

On 14/07/11 11:53 AM, Justin A. Lemkul wrote:
>
>
> 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
>>>> ============================================
>>>>
>>>
>>
>

-- 


"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
============================================