I am trying to simulate SPC/E water + 1 ion pair(K+Cl-) using SHAKE alogrithm for constraining bond and angle in water. I used the following input script
Have you done viz on your system? Are the 2 components (water
and other) moving as expected? Can you thermostat them individually
instead of together? If you can't figure it out and your data file is
small, please post it.
I visualized the system for 2ps . I see that there are only few molecules that are moving and also I see some ordered structure. I thermostated the two components ( water and ions) seperately, I did not see any difference. Please help me in figuring out. (I attached my data file to this email).
data.kcl_shake (241 KB)
I looked at your data file. It seems you mislabeled the atoms. E.g. in the “atoms” entry, you define atom 2 is oxgen and atom 1 and 3 are hydrogen, but in the “bonds” entry, you connect atom 1 and 2 (this is correct), atom 1 and atom 3 (this is wrong).
Thank you very much for your reply…
I corrected my mistake. Now it is working.