AMBER Archive (2008)

Subject: RE: AMBER: Initial Equilibration

From: Ross Walker (
Date: Thu Apr 10 2008 - 20:29:30 CDT

> I performed initial equilibration using following input. The
> main points are protein was restrained using weak force 5
> kcal/mol A2.
> I set initial temperature of 0K and set final temperature as 310K
> and it was 20PS run. When I checked the output of 20PS equilibration
> the temperature reaches only about 300K. Should I extend this
> equilibration step further before continuing to whole system
> equilibration without restraint. If I extend I feel I could use the
> last rst file as a starting point of extended equilibration
> or do you
> think it is better to submit a new equilibration job of ~40 PS.

There are two reasons it may not have reached 310K. The first is it didn't
have long enough, the second is that there was possibly some mistake in your
input file.

> tempo = 310.0,

This should be temp0 (as in temp[zero] and not tempo). Although this may
just be an email thing since I would expect sander to quit if you actually
had this in your input file.

As for continuing the unrestrained equilibration you need to think about
what it is you are trying to achieve here. The purpose of the initial phase
of MD is normally to relax away from a high energy position due to the
starting structure not being ideal. You want to do this in a controlled
fashion, hence the initial restraints to stop any large forces having too
much of an influence. At this point the temperature isn't really critical.
Thus the fact it didn't actually reach 310K is not really a problem.

You can now remove the restraints and restart the simulation from the
initial heating restart file. It will then start out around 304K or so.
There may be a small jump in the temperature early on due to the removal of
the restraints but this should equilibrate out fairly quickly. Leave temp0
set to 310K and then just look at things over the next 40ps or so.

I hope this helps

Good luck,


|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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