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

Alexander Alexander alexanderwien2k at gmail.com
Mon Aug 8 15:32:00 CEST 2016

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?


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
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