[gmx-users] Place water away from existing atoms

[Steven Neumann]

On Fri, May 18, 2012 at 12:30 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/17/12 4:45 PM, Steven Neumann wrote:
>
>>
>>
>> On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at 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<http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube>
>
> Also refer to the many posts in the mailing list archive on related topics.
>
> -Justin


Thank you. Using VMD I saw the trajecotry (nstxout =1) of my minimization
and the "water molecule which cannot be settled"  at step 35 split into
oxygen and two hydrogens which are app 8 A away from the Oxygen for the one
frame only (where the error occurs) then coming back in frame 36. How to
fix it? please, help

Steven

>
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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