GROMACS modification: Yes/No
I want to simulate water diffusion in poly electrolyte system. I have used two different water models tip4p and spc/e. I am using OPLS-AA force field. when I use tip4p water model I receive very good water diffusion coefficient with a straight MSD line while it is completely different for spc/e model(I used spc216 gro file for spc/e model). It is clear in the following images. What is the problem? Can I conclude that spc/e water model is not a suitable water model for my system or there is a deeper problem in my simulation?
Thank you for your kind response
How long were the simulations? TIP4P is known to diffuse quite a bit faster than SPC/E, so it will take longer for SPC/E to reach equilibrium.
Thank you very much for your reply.
It was 30 ns for both runs. Then it needs more time to reach equilibrium. I will try more times.
I have another question. Can I see polymer structure variations during these time periods? I mean more than 50 ns?
What Dr Lekmul pointed out is true. It is strange to see weird diffusion of water with SPC/E model. It is not as bad as you assume here. There could be some problem in your simulation. For polymer, 30-50 ns is nothing if you target to compute any polymer property. Possibly, you need to go into microsecond timescale simulations. Polymers are a kind of non-equilibrium systems, especially if polymers have long backbone chain. Best would be; you examine potential energy of your system and ensure that it has acceptable stability with time and does not drift significantly. In short, if one claims that he got equilibrium for a polymer system in nanosecond time scale, it is found to be highly unconvincing.
Fortunately, I got good results. I increased time to 100 ns and MSD plot changed to a straight line. I even checked potential energy it has acceptable stability. Although, I want to use Tip4p water model and also I took acceptable results from this kind of water model. But, showing different results when I used SPC/E was strange for me. Fortunately, I got good results too.
Thank you for your reply
When it comes to water models in general, it is worth considering what they are parametrised for.
In particular, SPC/E is designed to better describe the self-polarisation effect in bulk (i.e., pure) water. That can be interesting, but it is usually not what are aiming for in a system where the critical component is the interaction between water and some other molecule.
It doesn’t mean SPC/E is bad in itself (not to mention you can’t expect a 3-point water model to compete with a 4-point one), but if one wants to focus on interactions, SPC is arguably sometimes a better choice than SPC/E.