GROMACS version: 2019.3
GROMACS modification: Yes/No
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Recently I am using NPT ensemble to simulate the CO2-water-CO2 system during which a 10nm water slab is sanwiched by two CO2 gas slab. The forcefiled of CO2 is trappe and water is SPCE. I used virtue sites to control the rigid structure of CO2 by adding two dummy atoms. The boundary contion is periodic condition. The system has run more than 60ns and the system have already achieved equilibruim. However, when I run NPT simulation at 50bar and 373K , there appears a weird density profile of CO2 and the CO2 density isn’t symmetric. Do you know how to solve such problem?
Thanks a lot
CO2 density profile
What does it look like when you visualise the system? These density changes across the box should be obvious when looking at it. What do you expect it to do?
What density should CO2 under these conditions have when it is by itself?
Is SPCE compatible with TraPPE, and how should it behave under these conditions by itself?
Thanks a lot foe your reply.
I have checked the snapshots in VMD to view the CO2 distribution and it is consistent with the density profile having a peak in the left. For pure CO2 and water, the Trappe and spce can reproduce the bulk density very well. Maybe their combination results in such problem?
I have no idea if it is, but that is the first question you should be asking before using them together.
Note also, unless you are using non-PBC conditions, you will have a single block of CO2 and a single block of water. Along those lines, then the density value at both ends of the box should match, which they don’t appear to be.
I checked some literatures and it is reported that Trappe CO2 is compatible with SPCE water. In addition, I can make sure that I use the PBC condition in the simulation. I am thinking whether it is because of the software of gromacs. Although we use dummy atoms to control the rigid structure of CO2, does this treatment influence the interaction between water and CO2. Because for such system, people mainly use lammps. Lammps can control the rigid structure well through their algorithm.