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

[Justin Lemkul]

On 1/8/15 1:58 AM, Sridhar Kumar Kannam wrote:
> 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.
>

direction_periodic is the only geometry that ignores periodic distances.

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

No, it has been removed as of some time in the 4.6.x branch (clearly it's been a 
while since I used the pull code).  But in reality, you can find ways to make 
just about all the geometries behave like the others.  There are new options 
that replace the function of "position," as described in the manual.

-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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