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

[Victor Ma]

Thank you Justin.

Right now I have a sodium with three ligand residue. One of the ligand
residue is in a not very good position. I would like to apply a soft
harmonic distant restraint to keep them together and pull the "bad" ligand
residue a little closer. Mostly I am trying to maintain and optimize this
sodium-ligand cluster. What would you suggest? I am using Gromacs 5.0.4.
The "flat bottom restraints" and "intermolecular distance restraints" are
in the 5.1 version? Is "Any pull rate of zero maintains a specified
distance using a harmonic biasing potential. " what I need?

Thank you so much!!!!

Victor

On Tue, Sep 1, 2015 at 2:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/1/15 5:44 PM, Victor Ma wrote:
>
>> 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?
>>
>
> No, it wouldn't do that, but that's besides the point.
>
> 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?
>>
>>
> Any pull rate of zero maintains a specified distance using a harmonic
> biasing potential.  That's really what the "pull" code is - an external
> bias.  People often confuse this and think that is *must* induce some net
> change, but in fact it doesn't have to.
>
> I don't really know what your goal is here, but there are lots of ways to
> get around this - flat bottom restraints, intermolecular distance
> restraints, pull code, etc.  If you explain what you actually need to do I
> can probably be more specific with how to do it.  But a simple restraint
> really is just that - simple.
>
> -Justin
>
>
> 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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>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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