On 10/10/13 9:44 AM, Steven Neumann wrote:
Thanks. I will place them then within the distance from the box edge =
distance between atoms within the tube right? I can create bonds and use
harmonic spring constant like for backbone protein atoms...but whats the
point when they do not move anyway? I am using NVT.
If your goal is simply to have some series of atoms in a cylindrical overall
shape that do not move, there is no purpose to using bonds. NVT will still
suffer from problems with frozen groups; the temperature will not be right
because after a collision with a solvent atom, the tube atom by definition
cannot move.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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