Re: AMBER: &dipole input and some questions on using polarizable force fields

From: Seongeun Yang <>
Date: Wed, 31 Oct 2007 12:52:45 +0900

Thanks a lot for your reply.
I have one more important question on the issue you pointed out below.

> > Then, I equilibrat the system at the temperature of
> > interest uner NVT condition for a while until the density reaches the
> > appropriate value.
> I think you mistaken here: under NVT the density will not change, so it can
> never reach the "appropriate value".
The later part of what I wrote about density is definitely wrong, I know.
It applies to the previous step.

> > I didn't see any problem till now, even with "solvateoct" with
> > nonpolarizable force fields.
> As I said, I think you have been lucky. And the real problem is probably that
> your system is too small.
The important question is about the proper box size in md simulations.
I got no answer previously when I first post the question with other related ones.

I saw many articles where the box size is as small as just satisftying that the buffer size is only a half of nonbonding cutoff,
whether the system of interest is small oligopeptides or polypeptides.
The fact is that some of those articles are highly cited.
What do you think about this?

I understand that the larger buffer size is better for good results.
But I should choose an economic buffer size and 8.0 is not so a bad one if the nonbonding cutoff is 8.0 angstrom.
Am I wrong on this point, either?

I'm interested in using "solvateoct" to save computation time.
The usefulness of this option is to save computation time, right?
After I finish another runs following your comments, I'll post some more if there is any problem.

Thanks again.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Oct 31 2007 - 06:08:11 PDT
Custom Search