I tried to simulate a polymer-water-ion system. When I used tip5p water model and only the NVT ensemble, the simulation ran well but the whole complexes showed an obvious and large translation away from the unit cell from the trajectory visualisation. And it seemed all the components(polymer+water+ions) moved simultaneously. But I didn’t see such a large translation when I used tip4p water model.
The large translation seemed to contribute to a very large MSD value of the ions, which I think the system may show unphysical behaviours. I would like to know if there are some missing commands or arguments to control the system appropriately.
The input script is attached. The first and final frame of the trajectory are also attached. Any comments are highly appreciated! production.in (1.5 KB)
Please search the archives for “flying icecube”. You will find plenty of discussions of the phenomenon and possible solutions. Which works best for your case is difficult to predict.
It looks to me like your polymer block is being integrated as a single rigid body rather than a collection of rigid molecules. Please make sure each individual molecule in the polymer block has a unique molecular ID, and that the various types have been correctly specified (i.e. that types 26 to 28 really are TIP5P water).
Also, as a general note, a simulation with TIP4P water is really a completely different simulation to one with TIP5P water, even if all other coefficients are the same. A force field consists of all interactions used in a simulation, so those are really two completely different simulations. So – unless you are explicitly interested in the difference between water models as an MD development question – you should just stick to the water model that your polymer and ionic coefficients were parametrised for, and if you change water models you must ensure that your new, completely different force field reproduces the physical quantities used to fit the original force field.
