Hi Steven
You've tried with "constraints = none", but that still keeps constraints
over water molecules through SETTLE algorithm. Maybe you can try a
minimization with "define = -DFLEXIBLE" to remove settle over water and
then try again a constraint (settle) minimization.
Javier
El 18/05/12 12:58, Steven Neumann escribió:
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,
Steven
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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