Re: [gmx-users] simulating glass materials using GROMACS

[paul buscemi]

Use this site for starters  https://erastova.xyz/    it 
will move you toward your goal

Paul

> On Oct 12, 2019, at 2:03 PM, Alex Mathew  wrote:
> 
> Dear experts,
> I would like to simulate NASICON type glass using GROMACS. The paper I
> referred to here used LAMPP (https://pubs.acs.org/doi/abs/10.1021/jp5094349).
> How should I proceed for this kind of study with GROMACS?
> What kind of forcefield I can use in GROMACS? can anyone provide a starting
> point towards the simulation of materials using gromacs? (All the tutorials
> are devoted towards biological molecules).
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[gmx-users] simulating glass materials using GROMACS

[Alex Mathew]

Dear experts,
I would like to simulate NASICON type glass using GROMACS. The paper I
referred to here used LAMPP (https://pubs.acs.org/doi/abs/10.1021/jp5094349).
How should I proceed for this kind of study with GROMACS?
What kind of forcefield I can use in GROMACS? can anyone provide a starting
point towards the simulation of materials using gromacs? (All the tutorials
are devoted towards biological molecules).
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] Solid surface simulation and PBC issues

[Benson Muite]

On 10/11/19 6:41 PM, Samuel Asante Afari wrote:

Dear Users,
I am trying to simulate kaolinite in explicit water. After building my 
structure, I try to minimize it but I tend to get very high positive potential 
energy. After doing some research, one possible explanation is the broken bonds 
across the periodic boundary, which I notice in my surface model when I view in 
VMD. I have tried all that I can to fix it i.e using trjconv, whole, nojump, 
mol sequence and also adjusting box size. My question is, is the high potential 
energy caused by the broken bonds? Is this problem fixable by trjconv or it is 
a matter of topology? Which part of the topology cause this issue? Any 
suggestions to help me fix it?
Picture not attached. May want to post it online somewhere and put a 
link to it. It is not clear why you have broken bonds across the 
periodic boundary. What is you initial setup? Should kaolinite be at a 
low concentration? Are you able to use a bigger periodic box?


Thank you in advance

Sam

Please see attached my em.mdp and energy output.  Also attached is a picture of 
the structure with broken bonds.

integrator  = steep ; Algorithm (steep = steepest descent minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Minimization step size
nsteps  = 5 ; Maximum number of (minimization) steps to perform

; 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
cutoff-scheme   = Verlet; Buffered neighbor searching
ns_type = grid  ; Method to determine neighbor list (simple, grid)
coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb= 1.2   ; Short-range electrostatic cut-off
rvdw= 1.2   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions in all 3 dimensions
periodic_molecules = yes



Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 19 steps
Potential Energy  =  7.0229306e+05
Maximum force =  9.4779437e+02 on atom 522
Norm of force =  5.7396594e+02


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