AMBER Archive (2005)

Subject: RE: AMBER: density problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jun 01 2005 - 11:21:33 CDT

Dear Shulin,

> You say you heat your system up with constant volume to 100K or so at
> a very short run (2ps or less) .
>
> However, according to the Amber7 Users's Manual, at page 95 and
> page89, it is emphasieze that, it is important to equilibrate the
> temperature to sth like the final temperature using constant volume
> before NPT MD.
> In general, the final temperature is 300 K, if we just heating the
> system with with constant volume to 100K , will it bring any problem?

This is a topic for debate I feel. There is almost certainly more than one
way to do this...

The reason you shouldn't start out at 0K and constant pressure is that the
calculation of pressure is very inaccurate at low temperatures which means
the correction applied by the barostat will be huge. This leads to
instabilities and failure of the simulation. This is the reason you
typically heat with constant volume as suggested in the manual. The problem
with constant volume equilibration is that the initial water box generated
by LEaP has a density that is too low, typically 0.8g/cm^3. This is due to
the need to avoid bad contacts around the edges of the box when it is copied
in 3 dimensions in order to perform periodic boundaries. This typically
results in you obtaining small vacuum regions along the faces of the box.
This is particularly bad at the corners since 8 boxes meet here. When you
run constant volume you can form quite large > 5 angstrom diameter vacuum
bubbles or tunnels around these points. When you switch to constant pressure
it can take a very long time for these bubbles to dissipate. So, I tend to
run just enough constant volume to get to a temperature at which the
pressure calculation is accurate enough and then switch to constant
pressure. Once the pressure has equilibrated you can either remain at
constant pressure or switch back to constant volume. Note, this method gives
me the least problems, other's opinions may differ. Running constant volume
will not always lead to vacuum bubbles forming but if they do you will need
to go back and re-run the heating stage as I have suggested. Hence you can
avoid having to repeat work by following the protocol above.

Note, this problem is due to the initial water box not being dense enough.
Unfortunately this problem is not easy to solve with small systems since you
solvate the system and then selectively remove water molecules to get them
all within the box. This will always leave a vacuum region around the edge
of the box. Some changes to LEaP's solvation algorithm might improve the
situation, we are looking into this.

In the meantime you are probably safe to stick with what is suggested in the
manual but if you find your pressure does not equilibrate well when you
switch to constant pressure try looking at your system to see if you have
vacuum bubbles and if you do try the protocol I suggest.

That's my 2c. :-)

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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