[gmx-users] Analysis pull code simulation data to obtain Strain Stress curve

Md. Imrul Reza Shishir imrul.reza.shishir at gmail.com
Sat Mar 25 07:44:17 CET 2017

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.
> Alex
> 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
>> simulation.
>> 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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*Md Imrul Reza Shishir*
Master Student
*Inha University*
*CRC for NanoCellulose Future Composites*
36 Getbeol-ro, Yeonsu-gu
Incheon 21999
South Korea

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