[gmx-users] Place water away from existing atoms
s.neumann08 at gmail.com
Fri May 18 11:12:59 CEST 2012
On Fri, May 18, 2012 at 12:30 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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 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
>> 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.
Thank you. Using VMD I saw the trajecotry (nstxout =1) of my minimization
and the "water molecule which cannot be settled" at step 35 split into
oxygen and two hydrogens which are app 8 A away from the Oxygen for the one
frame only (where the error occurs) then coming back in frame 36. How to
fix it? please, help
> 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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