[gmx-users] Defining a limited space for the movement of Ion
jalemkul at vt.edu
Tue Aug 9 00:39:58 CEST 2016
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
> 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.
> 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
>>> 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 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
>> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users