[gmx-users] Analysis pull code simulation data to obtain Strain Stress curve
nedomacho at gmail.com
Sat Mar 25 08:16:39 CET 2017
Since you are not providing any details on your boundary conditions, or
whether you'd like to calculate the elastic modulus at a particular
temperature, or in the static approach, here's a general advice.
The potential energy of the system (per unit of sample cross-section)
associated with small strain is E = Y*eps^2/2, where E is the energy,
eps is the relative strain along a given axis (orthogonal to the
cross-section), and Y is the Young's modulus. The goal is to stretch or
squeeze the structure at different values of eps and plot the value of E
as a function of eps. If quadratic dependence is observed, you can
easily fit a curve with a given value of Y. Note that E is not absolute,
but the difference between what your simulation spits out and that
corresponding to eps = 0, i.e. the energy shift. Whether E comes from
energy minimization or as an average of a well-converged finite-T
simulation, this is a fairly standard approach (see, for instance, Fig.
S2 (a) of the supplement for
This works for solids. For softer polymers, you will have to try and
see. One can possibly use slow pulling to get the curve in one shot, but
I would use a scripted series of simulations, i.e. a loop like this:
1. simulate/relax the structure
2. save the final structure (coordinates and velocities, if dynamic)
3. use the structure from step 2, but rescale the box in a given
direction by, say 0.25%
4. repeat step 1.
From each simulation, assuming you properly extract your energy data,
you can obtain an average and get the entire result automatically.
On 3/25/2017 12:44 AM, Md. Imrul Reza Shishir wrote:
> Dear Alex
> My initial target to obtain nanomechanical properties of cellulose
> nanofibril. I have an 18 chain Cellulose Iβ structure of 20 residues. I
> want to obtain the young modulus of the fibril my molecular dynamics.
> But I am confused how I can approach to obtain this target.
> Thanks for the response. And wish some guidance.
> Best Regards
> Md Imrul Reza Shishir
> On Fri, Mar 24, 2017 at 5:35 PM, Alex <nedomacho at gmail.com> wrote:
>> Hi there,
>> Everyone is confused about how to get stress-strain curves from Justin's
>> tutorial. Because it has nothing to do with nanomechanics. Obtaining
>> Young's modulus from a particle-based simulation is quite elementary, if a
>> clear physical picture is present.
>> Please describe your system and explain what you are trying to achieve.
>> On 3/24/2017 2:15 AM, Md. Imrul Reza Shishir wrote:
>>> Dear all
>>> My target is to calculate nanomechanical properties (i.e. young's
>>> modulus/elastic modulus) from a strain-stress curve.
>>> For this purpose, I study Beven lab umbrella sampling pull code
>>> After that, I also run the same procedure simulation on my desire system.
>>> But I am now confused how I can obtain strain-stress curve from this
>>> simulation data.
>>> I want some guidance about this purpose.
>>> Thank you very much
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