Luis Miguel Medina Solano wrote:
Hello,
I used a -maxwarn 5, but I only obtain 1 warning, (about obsolete entries that
the .mdp file has).
I used a solute-box distance of 0.34 in order to reduce the simulation box. I used before a solute-box distance of 1 nm and the problem persist.
Don't reduce your box for convenience. You're certain to break the model
physics of your system, given the settings below, rendering probably any
simulation that might run invalid.
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention
Maybe this is unrelated to the underlying problem, but hopefully it helps in the
long run. Nothing worse than a reviewer saying, "Nice project, but 100% of the
data are junk."
my .mdp file is the next:
; VARIOUS PREPROCESSING OPTIONS
title =
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.004
In the absence of virtual sites, a 4-fs timestep is not likely to be stable,
even with LINCS, and certainly not at high temperature.
<snip>
fourierspacing = 0.24
This is double the "normal" value, meaning your PME calculations will be less
accurate than they probably should be.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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