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
--
========================================
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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