[gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

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

Also refer to the many posts in the mailing list archive on related topics.

-Justin

-- 
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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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