Dear Paul,

Great that you released your gcmc-code. I am currently testing it and receive error messages like “bond atoms missing” after a few MC steps. The used data file should be fine, at least it run without problems with my gcmc code. The data file describes a silica particle (molid=1) in the middle of the box where water (molid= 2,…,1539) can adsorb on its surface. Either there is something wrong in my in.gcmc file (I selected molid=2 as template) or the code messes up something with the molids. I do not know what is the problem here, but I for instance, at the beginning had the problem that molids were duplicated (more than one molecule with the same molid), what caused problems when I tried to delete such a molecule. I attached the data and in.gcmc that you could test it if you want.

Best regards


data_300000 (1.47 MB)

in.gcmc (1.32 KB)

Hi Sabine. Thank you for your interest in and testing of fix GCMC. I’ve seen similar errors when doing hybrid MD+MC simulations with typically-sized MD timesteps. After MC moves, the ensemble can be poorly equilibrated, so you might try smaller MD timesteps and/or just MC moves to start off. Or perhaps even try using the minimizer after a bunch of MC steps and prior to the MD steps.

Duplicated molids would definitely be problematic, so please make sure each molecule has its own specific ID.

More feedback on this is welcome, especially since the molecule capability for fix GCMC is still fairly new.