Re: AMBER: PME and counter ions

From: Lars Skjærven <>
Date: Thu, 20 Dec 2007 02:52:11 +0100

I'll try to answer your comments and questions below. Thanks for all
your replies so far :-)

Pablo Englebienne:
> addIons mol Na+ 250
> Why not using "addIons mol Na+ 0"? That would ensure that the system has
> a neutral charge... Did you get any warning out of LEaP?

As the net charge of my protein is -250 I would think adding 250
counter ions would neutralize the system in the same way as "addIons
mol Na+ 0". I basically used this syntax to underline the amount of
counter ions that were needed to neutralize the system.

Neutralizing this way yields no warnings from leap.

David Case:
> Of course I don't know why a 7500 residue system is "really unstable", but you
> should look (visually) at the distributions of ions you get. Also, it is
> certainly worth solvating *before* the addIons step: that is what I would
> recommend, and I don't know where in the manual it states otherwise(?).

I would not expect you to know why my system is unstable, or why the
simulation show unexpected behaviour. I am simply trying to figure out
which "method" to use for neutralizing systems (in general) that have
a high negative charge, as the system I am currently working with.
Explicit counter ions, or implicit plasma?

You state in an earlier post that "using a plasma might actually be
better than using explicit counter ions." Do you believe that this is
the case for systems no matter the charge of the system? If so, why,
and when, would you recommend to use explicit counter ions? I realise
this is not a straightforward question. I'll give it a try anyway =)

Section 3.6.3 (amber manual 9) suggests solvating after addIons
because of potential steric conflicts (waters/ions):
"If solvent is present, it is ignored in the charge and steric
calculations, and if an ion has a steric conflict with a solvent
molecule, the ion is moved to the center of said molecule, and the
latter is deleted. (To avoid this behavior, solvate after addIons.)".
Am I misinterpreting something here?

Looking at the distribution of the counter ions, would you say it is
"fine" if they are evenly spread around the protein?

Bill Ross:
> Also, how did you equilibrate? (Not sure if this was mentioned before.)

The minimisation is done in two steps:
a.) minimising water and ions around the protein (5000 steps)
b.) minimising the whole system (10000 steps)

Heating up to 100K in 20 ps using weak restraints and constant volume.
Heating up to 300K in 80 ps using weak restraints and constant pressure.
Equilibration in 300 ps using constant pressure.
Production runs with constant volume.

Does it seem reasonable? I will of course provide more details if that
would help..

Again, thanks for all your help.

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Received on Sun Dec 23 2007 - 06:07:12 PST
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