From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue May 15 2018 - 08:36:16 CDT
Hi Fateme,
Well, the whole system is artificial, since PBC isn't exactly physical. :) Frequently when I'm working with membranes, the lipids themselves carry a net charge, which the ions are set to counterbalance. If you only allow ions on one side of the membrane, you effectively create a net dipole in the membrane (net negative lipids, and net positive ions only on one side), which due to PME, effectively means that the net dipole is repeated unto infinity. Is this a problem? Maybe. Maybe not. I don't restrain my ions, so I haven't thought about the implications, but I suggest that you do, and to see how others have handled this in the literature.
-Josh
On 2018-05-15 02:41:11-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
Josh
Thanks for replying to my question. I've turned off warpAll and it did work--_000_DM6PR09MB29222731360DC0DBE871030BE4930DM6PR09MB2922namp_--
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:07 CST