Re: Is it necessary to neutralize the system with NAMD program?

From: Jérôme Hénin (
Date: Fri Mar 19 2004 - 04:39:06 CST

Actually, it would really help to have the opinion of someone with a good
knowledge of the PME implementation in NAMD about how it is supposed to
behave with a charged periodic box.

Jim, maybe ?

Thanks in advance for any contribution on that matter

Le mardi 16 Mars 2004 20:07, Brian Bennion a écrit :
> I read the same email message on ccl.
> I have thought about this problem as well and have tested systems both
> ways.
> I was taught that ions, unless specifically needed in the protein
> structure, were superflous. The water screens the charge on any ion
> within 4-6 angstroms. However, these simulations were not using PME.
> My results with and without counterions are equivalent. (ie temp, pres,
> gpress values are within 1-2% at 0.25ns and 11.0ns for a system with 65K
> atoms and a net +3 charge.
> If any one else has a contrary info I would love to here it.
> If you choose to add counter ions, the vmd plugin autoionize might be what
> you need.
> Regards
> Brian
> PS
> Contrary to what the ccl list member said. We are not even close to
> real-life conditions even without PBC. Thats what ab-initio MD is for!!

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