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

[Sridhar Kumar Kannam]

Hi Justin,

Thanks for your help. I am using the pull code with below settings ...

pull                               =   umbrella
pull_geometry            =   distance
pull_dim                      =   Y Y N
pull_group1                =   Protein
pull_start                     =   yes
pull_rate1                   =   0.0
pull_k1                        =   1000

My simulation box dimensions are  10, 10 and 20 nm along the x, y, and z
directions (x:0-10, y:0-10, z:0-20 nm). The centre of my protein is at 5.0,
5.0 and 10.0.
I want to constraint the protein centre to 5.0 and 5.0 in the x and y
directions and left free in the z direction.

With the above pulling code, I got the following error - Distance of pull
group 1 (7.0711 nm) is larger than 0.49 times the box  size 10.0
I have modified the box size in gro file to 20, 20 and 20 nm. This would
not effect the results as I have solid walls at the boundaries. With this
set up, the distance between the protein centre and origin of pull_group0
(0, 0, 0) is kept constant during the simulations. Even though this is not
exactly the same as constraining the protein CM to its initial position (5,
5, 10) I am ok with it.

Now my question is, can I avoid modifying the box size ? I have many
systems with different sizes. Manually changing the box for each simulation
is not desirable.

pull_geometry          =  direction-periodic  avoid this problem but does
not keep the distance of the protein from the origin (0, 0, 0) fixed.


Thank you...





















On Fri, Nov 28, 2014 at 1:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/26/14 6:32 AM, Sridhar Kumar Kannam wrote:
>
>> Thanks Justin,
>> I agree its not a basic need, but an easy to implement (for the
>> developers)
>> and useful feature.
>>
>> I have added the below code to my mdp file.
>>
>> pull                      =  umbrella
>> pull_geometry   =  distance
>> pull_dim             =  Y Y N
>> pull_start            =  yes
>> pull_ngroups     =  1
>> pull_group0       =  Protein
>> pull_group1       =  Protein
>> pull_init1            =  0.0
>> pull_rate1          =  0.0
>> pull_k1               =  1000
>>
>> Here, I am trying to constrain the CM of protein in x and y directions.
>> The
>> protein should be free to move in the z directions and rotate.
>>
>> The simulation is running fine without the pull code included but
>> including
>> the pull code resulting terminating the simulation with out any warnings
>> or
>> error messages. Is my code correct or am I missing anything ?
>>
>>
> You can't have the same group serve as both reference (group0) and
> restrained (group1) group.  I'm surprised grompp didn't totally fail.  If
> you want an absolute restraint (not constraint, since it's only a bias)
> then pull_group0 should be empty and pull_group1 would be the protein.
> Heed the resulting grompp warnings about artifacts.
>
>
> -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 :)