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

[Sridhar Kumar Kannam]

Thanks Justin,
Finally this is working.

pull                               =  umbrella
pull_geometry            =  position
pull_dim                      =  Y Y N
pull_group1                =  Protein
pull_group0                =
pull_ngroups              =  1
pull_rate1                   =  0.0
pull_k1                        =  5000
pull_start                    =  yes


Is there an option to avoid this error: Distance of pull group 1 (7.0711
nm) is larger than 0.49 times the box  size 10.0
without increasing the box size ?  In my system the protein is constrained
to the pore axis which is at the mid point of simulation box.

The option pull_geometry=position is removed from the 4.5 version, right ?
or is it only missing from the manual ?

Best,




On Thu, Jan 8, 2015 at 3:52 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/6/15 9:48 PM, Sridhar Kumar Kannam wrote:
>
>> 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) ?
>>
>>
> Restraining the protein COM to be coincident with the pore COM is indeed
> the best way to do this; probably "distance" geometry is not the right way
> to go, though.  Try "position" (and other applicable modifications to other
> settings) instead.
>
>
> -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 :)