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

From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
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
Jerome

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!!
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:27 CST