Dear all,
I mean to use deform for applying shear rate on my system, but, I could not find any tutorials on this regard.
Could you please tell me how I can do deform by gromacs (step by step please)?
And, How can I understand if a proper shear rate is applied?
These questions are really serious to me as I need to apply shear rate in my project.
I apperciate your responses in advance,
Best regards
Hi,
the deform option has to be defined in the mdp file (Molecular dynamics parameters (.mdp options) — GROMACS 2021.1 documentation) There you define the directions along which you want to deform (by putting the value of the rate [nm ps-1] you want to use for that directory). The other values has to be set to zero. The values of the rate is problem specific, thus I can just suggest to have a look in literature.
The option deform can be combined with isotropic and anisotropic pressure (Molecular dynamics parameters (.mdp options) — GROMACS 2021.1 documentation). the pressure type is also defined in mdp file.
Before applying deformation, it is good to have an relaxed and equilibrated system, that you achieve using standard NPT or NVT MD simulation for example.
Best regards
Alessandra
Dear Alessandra,
Thanks for the informative response.
I mean to write in the .mdp file deform (shear rate) and electric field (voltage) in x-axis direction.
In this regard, is the command below correct?
;voltage
electric-field-x = 0.02 0 0 0
;deform
deform = 0 0 0 9 0 0
But, I am really concerned about deform being non-equilibrium simulation and its need to use isotropic and anisotropic pressure.
In addition, could you please tell me if deform can be applied along with electric field?
I am not aware of how to handle these with each other.
I apperciate your assistance in advance and I hope you have time to consider these questions.
Best regards
I seriously doubt such a combination has been tested. Tread carefully as you may get unexpected results.
Dear Prof. Lemkul,
Many thanks for your response.
As you mentioned, I am not really aware of results I would have.
But, I will try it out as a short time simulation about 5-10 ns.
Could you please help me with this, if you have experience of combining several .mdp options?
And, could you please tell me if deform and electric field can be probably combined in a simulation run?
Best regards
I have no relevant experience with either option, and certainly not in conjunction. But I’m noting that the code combinations are likely not tested and you should (as with any good scientific approach!) deal with a known system first, so you can confirm expectations. If you can’t do that, you’ll need to go into all the relevant code and make sure the options play nice. That’s honestly pretty daunting. But the fact that this is the first time in about 15 years of using GROMACS that I’ve ever seen anyone ask about the combination of these options suggests that you should be very wary of just jumping in and running such a simulation without substantial and robust testing before even approaching your system of interest.
Hi Alessandra,
I hope you are good.
I found most of your responses very informative on this platform.
Actually i want to know the relationship between strain rate defined in most of literature and deform values in mdp file (in nm/ps) (in literature the strain rates are quite large value e.g. 2 E10 per second or 1 E 7 per second) how to convert the literature defined strain rates into the deform value which we must define in mdp file for that corresponding strain rate?
For example, if i want to do stress-strain analysis by increasing z-dimension of simulation box at a strain rate 2E10 per second for a period of 5 ns in simulation
can you please write what deform value, compressibility and pcouple type i should specify for this ?
Your kind response will be highly appreciated.
Best Regards
Saiqa