[gmx-users] restraint the CM of a molecules in any one of the directions.
Sridhar Kumar Kannam
srisriphy at gmail.com
Mon Jan 5 04:54:51 CET 2015
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.
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
>> 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.
>> protein should be free to move in the z directions and rotate.
>> The simulation is running fine without the pull code included but
>> the pull code resulting terminating the simulation with out any warnings
>> 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 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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Sridhar Kumar Kannam :)
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