AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 10 2009 - 12:58:15 CDT

Sally- I got your files.
can you redo rune after changing ntcm to 0, and also try switching back to
Berendsen thermostat (ntt=1)?
try them separately. it may be that in run2 the molecule was recentered, and
the refc was not. in general combining positional restraints with removal of
center of mass motion can be dangerous. we have better checks in more recent
versions of Amber
carlos

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

> 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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