AMBER Archive (2005)

Subject: Re: AMBER: REM difficulties

From: Peter Varnai (pv232_at_cam.ac.uk)
Date: Thu Nov 03 2005 - 13:26:11 CST

Thanks for the response.

> > * in my particular case using default i/o I have problems with mixed
> > ext 000/001 (although in test it seemed to be OK):
> >
> are you writing replica outputs or temperature-based outputs?

I used the default as in the test, that should be for a given
temperature.

> the code cannot handle the same temp0, this exchange is temperature-based
> so you end up dividing by zero if they match. Amber9 will check the inputs for
> this.

sander seems to run; delta remains zero, but I did not see division
with delta.

> It's not clear excatly what you mean by the last statement.
> Did you get a "run2.out.000" file? Did you get one called
> "run2.out.001"?
> I haven't seen any similar behavior myself (e.g. having multisander
> not output files from each "group member").

again, at the same temp0 (that I should not use) only run2.out and
run2.out.000 are produced not run2.out.001. run2.out is supposed to be
the results before the first exchange that is discarded?

> What happens if you leave out the "-rem 1" flag?

I could not get replica exchange using groupfile with or without the
"-rem 1" flag.

Peter

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