AMBER Archive (2009)

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

From: Sally Pias (sallypias_at_gmail.com)
Date: Fri Jul 10 2009 - 12:20:27 CDT

On Fri, Jul 10, 2009 at 11:02 AM, Carlos
Simmerling<carlos.simmerling_at_gmail.com> 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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