Pulling a box in X-direction at a constant rate for calculating Young's Modulus of a solid

User discussions
1

GROMACS version: 2020.7
GROMACS modification: No
Hi,
I am currently trying to pull a box in X-direction with these settings in my mdp

tcoupl                   = v-rescale 
tc-grps                  = System
tau_t                    = 1.0  
ref_t                    = 310   
Pcoupl                   = parrinello-rahman 
Pcoupltype               = semiisotropic
tau_p                    = 12.0  
compressibility          = 0 3e-4
ref_p                    = 1 1

gen_vel                  = no
gen_temp                 = 310
gen_seed                 = -1

; options for deform
deform = 3e-7 0 0 0 0 0
refcoord_scaling = com

Are these settings fine if I want to pull the box in X-direction with this deform rate of 3e-7 nm/ps? Also, since my molecule rotates/translates a lot, do I need to fix my molecule and pull it? Or, it’s fine to pull the box even if the molecule is performing these motion. FInally, if I want to pull the molecule in x-direction, is it necessary to have this molecule aligned at this particular direction at first, and have the box created with x and y length equal to the respective x and y length of the molecule so that the molecule just fits inside the box. BTW - I am doing a CG MD simulation. Thanks.

2

From your post it is not clear what you want to achieve.

The deform options applies a shear deformation to the unit cell. You should (only) use this if you want to apply a shear.

3

Hi Hess, so this mdp settings are correct for calculating the sheer modulus, if not for Elastic modulus of a solid right? Thanks.

4

I see now that my answer was not accurate. You are modifying a diagonal element of the unit cell. So if your system is a solid, you can compute the elastic modulus from the strain and the observed pressure.

But I still do not understand your other questions.

1 Like
5

Thank you Hess. Another question was in relation to the alignment of the molecule, which I guess should be redundant. So, if I want to compute the elastic modulus of my solid, are the mdp settings I have given fine? I guess, instead of using just one molecule, I should add a number of molecules in a box with water. Am I following correctly in here? Thanks.