[gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

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

-- 
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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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