[gmx-users] atom moved too far

Justin Lemkul jalemkul at vt.edu
Fri Jan 3 02:48:14 CET 2020



On 1/2/20 3:02 PM, Christos Deligkaris wrote:
> thank you Justin.
>
> I saw on your umbrella sampling tutorial how to implement the restraints
> using the pull code.
>
> The protocol I used is (if I understand correctly your question): The
> energy minimization reached the cutoff for maximum force 1000 in 346 steps.
> My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 NPT
> equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT
> equilibration time 500ps) where I slowly decreased the position restraints
> on DNA and the small molecule, as well as the harmonic restraint between
> the two.
> What are the best temperature coupling groups to use when we are not
> certain whether the small molecule will spend the entire simulation period
> physically bound to the macromolecule or whether it will become fully
> solvated at some point? Is Macromolecule and Non-macromolecule the best
> option since the small molecule will always (to a small or large extent)
> interact with water (versus the Macromolecule_and_small_molecule and
> everything else grouping option)?

I doubt there would be a measurable or provable difference between the 
behaviors of the two setups.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================



More information about the gromacs.org_gmx-users mailing list