temperature effect of polymer deformation


I am deforming a polymer in x direction under uniaxial loading using fix deform. I am using nvt dynamics. This is a coarse grain model. There are 25 beads (one bead is one monomer) in a chain and there are total 36 chains. The deformation rate is 1e-5. My stress strain curve is quite similar to the experimental figure but my problem is with the temperature which is 1 K and the experimental value is at room temperature 298 K. I can't increase the temperature more the 1K. If I increase it, even at 2K or 5K, the stress level is very low (close to zero) and getting some fluctuation only.

1. I thank for your help before about the free energy and potential energy tips. Is this the problem of free energy that doesn't allow me to increase temperature?

2. As your previous suggestion, using temperature close to zero i can avoid the free energy calculation. So, would you please help me to know that can I compare my zero temperature simulation with the room temperature experiment?

3. I have collected the book of "Free Energy Calculation by Andrew Pohorile" but before starting that book, I am not getting how my stress (I am taking pressure tensor as stress) is related to the potential energy or free energy. If you please give me some hints in a few sentence then I could start learning about free energy calculation.

Would anybody please help me to know if I am doing anything wrong or how can I increase the temperature to the room temperature?

Best Regards

Md Salah Uddin

If you are using fix deform and fix nvt, then you
need to be sure you are thermostatting the thermal

motion and not the full velocity. By applying
a bias to the thermostat that removes the deformation
velocity, e.g. via compute temp/deform. See

Section 6.16 of the manual for details on biasing