AMBER Archive (2008)

Subject: Re: AMBER: Volume of ucell too big

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 30 2008 - 00:19:31 CDT

On Wed, Jul 30, 2008, baohua zhang wrote:
>
> I executed sander program to run MD . My organic molecule solvatebox watbox
> 13102 ,and the system size is :60.8870240 56.5703430 50.1236310
> 90.0000000 90.0000000 90.0000000
> But I got the following error message in output file.
> NSTEP = 545800 TIME(PS) = 961.200 TEMP(K) = 537.93 PRESS =
                                                        ^^^^^^^^

> Density = 0.3301
                                                      ^^^^^^^^^^^^^^^^^^^^^

You have a very high temperature, which looks like it is causing the system
to expand to a very low density, probably very rapidly. Amber is not set up
to handle drastic volume changes (such as in turning liquid water into steam).
You probably need to figure out why the temperature is so high.

...dac

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