I suggest you first can run a system with only polymer solution in NPT ensemble. After a suitable density is reached, then you can add two graphite sheets into the equilibrated system, please set the distance between graphite and solution carefully (or trial error).
Best wishes, Zhongqiao Hi, Thanks a lot for the suggestion! NPT does is difficult with the frozen graphite layers. On the other hand, I have also done another simulation using the implicit graphite wall with the same polymer solution (composition and system volume). These implicit wall systems seems good, at least the empty space is not there. Any other idea about it? best regards, Baofu Qiao chris.ne...@utoronto.ca wrote: > Sounds like a bubble. Do some NpT equilibration by adding pressure > coupling. That's going to be difficult with your freeze groups though. > Basically, you need to find a way to get the correct solution density > between the graphite layers. > > -- original message -- > > Hi all, > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
