[gmx-users] Place water away from existing atoms
Justin A. Lemkul
jalemkul at vt.edu
Fri May 18 01:30:50 CEST 2012
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
> 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?
Also refer to the many posts in the mailing list archive on related topics.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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