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

[Alexander Alexander]

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
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?

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

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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