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

[Sridhar Kumar Kannam]

Hi Justin,

Few weeks back I tried flat-bottom restraints also. It did not work as the
inner and outer cylinder radius are equal and very small (to keep the
protein close to the pore axis).

Based on your tutorial on Umbrealla sampling I am using the below pull
code.  The nanopore (and hence its centre of mass) is fixed in my
simulations.

pull                               =  umbrella
pull_geometry            =  distance
pull_dim                      =  Y Y N
pull_group1                =  Protein
pull_group0                =  Nanopore
pull_ngroups              =  1
pull_rate1                   =  0.0
pull_k1                        =  5000

pull_init1                     =  0.0
pull_start                    =  yes

The reference CM co-inside with the pore axis, to which I want to constrain
the protein. When I run the simulation, the protein is moving quite a far,
2 to 3 nm from the axis.
With the above pull code we expect the protein to stay close to the pore
axis, i.e., can we restrain the CM distance between the two groups protein
and nanopore (which in this case is zero distance) ?

Best,






On Tue, Jan 6, 2015 at 10:13 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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-- 
Cheers !!!
Sridhar  Kumar Kannam :)