[gmx-users] Water molecule cannot be settled
s.neumann08 at gmail.com
Fri May 18 14:31:01 CEST 2012
On Fri, May 18, 2012 at 12:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
>> emtol = 1000.0 ; Stop minimization when the maximum force <
>> emstep = 0.001
>> nsteps = 50000 ; Maximum number of (minimization) steps to
>> 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,
>> rlist = 1.4 ; Cut-off for making neighbor list (short range
>> coulombtype = PME ; Treatment of long range electrostatic
>> 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
>> 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
>> 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.
Thank you. I tried without water and it works really fine. However, the
posted mdp with water was with the emtol = 1000 - then NO errors occur.
When I decrease it to 100 then this error appears. I will try to process it
to NVT and see how it goes.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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