[gmx-users] Defining a limited space for the movement of Ion

[Justin Lemkul]

On 8/8/16 9:31 AM, Alexander Alexander wrote:
> Thanks for your suggestions.
>
> Can you please confirm me that the reference position in the spherical
> flat-bottom restraint should be defined in a separated file passing by "-r"
> from grompp. Since I want that the Ion accompanies the molecule in the

Yes.

> whole simulation, then I was wondering if this reference position also is
> allowed to move(sphere also moves) as well or it is just a fix position as
> center of sphere? How can I make a relation between this reference position
> and molecule?
>

The reference position is the coordinates themselves, scaled by refcoord_scaling 
if using pressure coupling.  If the protein drifts significantly over the course 
of the simulation, this may not achieve what you want, without an additional 
restraint on protein COM motion (which can also be done).

> If I want to use the pull code to do so, I was wondering how tight the
> spring should be (the force constant) approximately?
>

No idea offhand.  There are no hard rules here.

-Justin

> Thanks,
> Regards,
> Alex
>
> On Mon, Aug 8, 2016 at 1:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/8/16 7:10 AM, Alexander Alexander wrote:
>>
>>> Dear Gromacs user,
>>>
>>> I have defined a "molecule = A" and a single ion together as
>>> "[moleculetype] = A + Ion" in my simulations. But, I get some problem when
>>> Ion goes so far away from the molecule A, because physically I would have
>>> a
>>> separated molecules defined as [moleculetype], so, I want somehow keep the
>>> Ion close to the molecule in simulation, I mean just in physically
>>> meaningful-limited sphere around the the molecule.
>>> Would you please let me know how I can do that?
>>>
>>>
>> Use either the pull code or a spherical flat-bottom restraint on the ion.
>>
>> -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

==================================================