[gmx-users] restraint the CM of a molecules in any one of the directions.

[Justin Lemkul]

On 1/5/15 9:31 AM, Sridhar Kumar Kannam wrote:
> Hi Justin,
>
> Please see Figure 1 of the attached paper. I have a SiN nanopore/membrane with
> the solvent on both the sides. The protein is inside the pore as in Figure 1a.
> Let say the pore axis is along the z-axis.  I want to constraint the CM of the
> protein to pore axis in the x and y directions.  The protein should be able to
> move freely along the z-direction but should be constrained/restrained at the
> pore centre in  x and y directions.
>
> I can do this in NAMD but is there a way to achieve this in Gromacs ?

Try flat-bottom restraints.  If that doesn't work, well, if it works in NAMD...

-Justin

-- 
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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

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