[gmx-users] how to apply distance restrains between a residue and an ion
jalemkul at vt.edu
Tue Sep 1 23:51:05 CEST 2015
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.
> Thanks again!!
> 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
>>> 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
>>> [ 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
>> 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 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
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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
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