RE: RE: Hard wall on Z direction for ions

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_--

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