[gmx-users] Place water away from existing atoms

[Steven Neumann]

On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul <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?

>
> --
> ==============================**==========
>
> 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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