On 11/3/13 12:38 AM, Gianluca Interlandi wrote:
Is it possible to use position restraints:
define = -DPOSRES
during an energy minimization? I tried to do that but it looks like all atoms
are moved during minimization:
Depending on the forces present in the system, it is possible that the atoms
will still move. Position restraints do not prevent motion, they provide a
biasing force that disfavors motion. If the forces between your atoms are such
that they overcome the bias, then indeed the atoms will move.
If you don't want them to move at all, then freeze them or use a stronger force
constant for position restraints. Doing so generally defeats the purpose of
minimization, though.
-Justin
; VARIOUS PREPROCESSING OPTIONS =
title =
cpp = /lib/cpp
include =
define = -DPOSRES
; IMPLICIT SOLVENT OPTIONS =
implicit-solvent = GBSA
gb-algorithm = OBC
; RUN CONTROL PARAMETERS =
integrator = steep
; start time and timestep in ps =
tinit = 0
dt = 0.001
nsteps = 1000
; ENERGY MINIMIZATION OPTIONS =
emtol = 0.00001
emstep = 0.01
nstcgsteep = 1000
Thanks!
Gianluca
-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
--
==================================================
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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