On 5/17/12 4:45 PM, Steven Neumann wrote:
On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
On 5/17/12 11:50 AM, Steven Neumann wrote:
My tube is finite. I increased my box so the water could interact with
all water
molecules. The same problem: My minim.mdp
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 10.0 ;
emstep = 0.001
nsteps = 50000 ; Maximum number of (minimization) steps to
perform
nstxout = 1
; Parameters describing how to find the neighbors of each atom and how
to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long
range forces
ns_type = grid ; Method to determine neighbor list (simple,
grid)
rlist = 1.4 ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1.4 ; Short-range electrostatic cut-off
rvdw = 1.4 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
Well... no clue...
Then the diagnostic tips I listed before still apply, as well as those
listed on the webpage linked from what I posted earlier.
-Justin
Thank you Jusin! By the way, how can I create infinite tube in gmx?
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
Also refer to the many posts in the mailing list archive on related topics.
-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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