[gmx-users] Place water away from existing atoms
s.neumann08 at gmail.com
Thu May 17 22:45:59 CEST 2012
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
>> emtol = 10.0 ;
>> 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)
>> 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.
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
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