[gmx-users] how to apply distance restrains between a residue and an ion

[Victor Ma]

Hello Justin,

Thanks for the response!! I know how to set up the pull code. But using
pull code ("umbrella") would keep pulling the two together causing unwanted
clashes and non-physical scenario. How can I get around with that?
If I set the pull-coord1-rate = 0 and  pull-coord2-k = 100, for example, is
this equal to a harmonic distance constraint without the "pulling" part?

Thanks again!!

Victor

On Tue, Sep 1, 2015 at 2:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/1/15 2:54 PM, Victor Ma wrote:
>
>> hello all
>>
>> I need to apply a distance restraint between a sodium and a residue. I
>> read
>> the manual, etc, which seems to suggest adding something like below to the
>> .itp file.
>>
>> [ distance_restraints ]
>> ; ai aj type index type’ low up1 up2 fac
>>    10 16 1    0     1     0.0 0.3 0.4 1.0
>>    10 28 1    1     1     0.0 0.3 0.4 1.0
>>
>> But my protein and ions are in two separate itp file. So how do I do it?
>>
>> Also I have multiple sodiums, but in the SOD.itp file, there is only one
>> line
>> [ moleculetype ]
>> ; name  nrexcl
>> SOD          1
>>
>> [ atoms ]
>> ; nr    type    resnr   residu  atom    cgnr    charge  mass
>>       1        SOD      1      SOD    SOD      1      1.000    22.9898
>>   ; qtot  1.000
>>
>> So how do I get the atom number for the specific sodium I want to
>> restraint?
>>
>>
> Either you need to use the pull code (simple harmonic restraint) or if you
> need the flat-bottom nature of the distance restraints, you need to place
> the [distance_restraints] directive under an [intermolecular_interactions]
> directive and use global atom numbers.  This feature is only available in
> version 5.1.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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