On 5/18/12 6:58 AM, Steven Neumann wrote:
Dear Gmx Users,
My system consists of a Tube made of Oxygen, Hydrogen and ions. These atoms are
not connected via bonds. I try tu run EM:
; 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 = 1000.0 ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
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)
freezegrps = TUB
freezedim = Y Y Y
Then a lot of errors "water molecule on atom X cannot be settled". I tried:
1. constraints = none
2. remove those water molecules - then other water molecules have the same error
3. using nstxout =1 in VMD, I could observe that some of the molecules facing
this error split in one frame (hydrogens 7A away from oxygen) or spin around 180
degrees - it depends.
4. I tried increase vdwradii of the atoms which form my Tube so they wont
overlap with water
If you have any suggestions I will really appreciate,
This is starting to sound more and more like a topology instability. Can you
successfully run EM on your tube in the absence of water? If not, then the
problem is with the definition of the tube, with the water problems being a
consequence.
-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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