AMBER: Question about using PMEMD and GB

From: H W <>
Date: Wed, 6 Sep 2006 13:41:12 -0400


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!

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Sep 10 2006 - 06:07:05 PDT
Custom Search