[gmx-users] restraint the CM of a molecules in any one of the directions.
Sridhar Kumar Kannam
srisriphy at gmail.com
Thu Jan 8 07:58:45 CET 2015
Finally this is working.
pull = umbrella
pull_geometry = position
pull_dim = Y Y N
pull_group1 = Protein
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 ?
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
>> 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
>> 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 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
Sridhar Kumar Kannam :)
More information about the gromacs.org_gmx-users