AMBER Archive (2007)

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

From: David A. Case (case_at_scripps.edu)
Date: Tue Oct 30 2007 - 09:58:20 CST

On Wed, Oct 31, 2007, Seongeun Yang wrote:

> When I heat the system to temperature of interest, I use NPT condition.

This is dangerous. You may have been lucky in the past, but generally you
should use NVT first, to get a good temperature, then use NPT.

> 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".

> 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.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu