On 11/26/12 6:01 AM, SANTU BISWAS wrote:
On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS <santu.biswa...@gmail.com> wrote:
dear users,
When performing a energy minimization of a
polypeptide(formed by lysine-5-residues) in vacuum box by using
Steepest Descent and also Conjugate Gradient methods in gromacs double
precision,i noted that GROMACS never converges to emtol values under
about 0.00001 kj/mol/nm.I have used the .mdp file which is given below
title =
cpp = /lib/cpp
;include =-I../top/
define = -DFLEXIBLE
; RUN CONTROL PARAMETERS =
integrator = steep
; start time and timestep in ps =
tinit = 0
dt = 0.001
nsteps = 1000
rlist = 0.9
rcoulomb = 0.9
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw_switch = 0
rvdw = 0.9
; Neighbour searching
nstlist = 1
; ENERGY MINIMIZATION OPTIONS =
emtol = 0.00001
emstep = 0.1
nstcgsteep = 1000
Are you using single or double precision? Single precision steepest descents is
unlikely to ever reach such a low emtol. Double precision and more thorough
methods (CG and/or L-BFGS) may achieve it, perhaps after several rounds of each.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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