AMBER Archive (2006)

Subject: AMBER: Question about using PMEMD and GB

From: H W (howardww_at_gmail.com)
Date: Wed Sep 06 2006 - 12:41:12 CDT

Hi,

I want to use PMEMD and GB to simulate a protein, with flag igb=2.
Should I set ntb=0? On the manual it says "no periodicity is applied
and PME is off. But I want to use PME+GB to do the simulation.

Another question is, do I need to add counter ions to the system? When
I add counter ions, say two Na+, they just go away and cause restart
file crash.

Thanks for any advise!

Howard
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