AMBER Archive (2009)

Subject: Re: [AMBER] unexplained blow-up at restart

From: Carlos Simmerling (
Date: Fri Jul 10 2009 - 12:25:10 CDT

Sally, can you email me directly both md output files?

On Fri, Jul 10, 2009 at 1:20 PM, Sally Pias <> wrote:

> On Fri, Jul 10, 2009 at 11:02 AM, Carlos
> Simmerling<> wrote:
> > is the refc the same as for the first run? the restraint energy here
> should
> > be roughly comparable to the end of run 1, since you used the same mask.
> Yes, I just checked to verify that the refc is the same (in case there
> was an error in my script). They are identical. I also did a careful
> comparison of energies between the first step of md2_NPT and the last
> step of md1_NPT. The only notable differences are in the restraint
> energy and the potential energy (presumably because of the major
> change in the restraint energy). I should note that the single-step
> output md2_NPT run uses a Langevin thermostat, while the md1_NPT run
> uses Berendsen temperature control. However, I have seen roughly the
> same output using both thermostats for md2. Now I am quite puzzled.
> Any suggestions on what I might check next?
> Thanks,
> Sally
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