[gmx-users] restraint the CM of a molecules in any one of the directions.
Sridhar Kumar Kannam
srisriphy at gmail.com
Wed Nov 26 12:32:12 CET 2014
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 ?
On Tue, Nov 25, 2014 at 11:52 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 11/24/14 7:13 PM, Sridhar Kumar Kannam wrote:
>> Dear Users,
>> I am just resending the email.
>> Constraining the CM of a molecules is a basic need of MD. Is that feature
>> not available in Gromacs ?
> You can accomplish something like this with the pull code, using no
> reference group, so each restraint is in terms of absolute coordinates, but
> you can accumulate artifacts with pressure coupling. This would generally
> be somewhat uncommon, since absolute positions within a periodic system are
> arbitrary, anyway, so I wouldn't call it a "basic need" for most
> 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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