Hi
I run MD simulation for 15LI and 15TFSI ion in 15 (PEO with 90 EO monomers) polymer electrolytes. and calculated MSDs using gmx msd gromacs command.
- But I get a very noisy curves even after running a very long run time simulation. what can be the reason for it?
- secondly the absolute values on y-axis are also very less as compared to the reference literature i am following which makes my calculated diffusion coefficient for Li and TFSI ONE POWER LESS than reference literature.what are the possible reason for this? There is something wrong with my system or my calculation method?
3 when i use -mol option with gmx msd it didnot plot msds for individual molecule/ion for me i only get one same curve which i am geting without -mol option. why is this ?
i am attaching my MSDs curve with varrying salt concentration and calculated diffusion coefficient.
please suggest me what should i change in my system or my calculation method
