On Wed, 2014-04-23 at 12:15 +0200, Fabiana Caporuscio wrote:
>
> Dear Amber
> users,
>
> I am
> experiencing a problem that has been already reported in the list, but,
> unfortunately, I was not able to find out a solution among the replies.
>
> I run some
> tests with the Amber10 version of xmin and I found that the xmin minimizer
> stops before it reaches either maxcyc or drms. I tried different drms and
> maxcyc values but minimizations always stop at the same step returning the same
> results. At every step RMS=0.0 values are reported except in the 'FINAL
> RESULTS' section. This is one of my input files:
Amber 10 is ancient in computer software years and has not been
realistically supported since probably ~2010 or 2011. Please upgrade to
the latest version of AmberTools 14 (very few of us even have a copy of
Amber 10 that we can run tests on).
>
>
>
>
>
>
>
> &cntrl
>
> ntb=0, ntmin=3, maxcyc=5000, drms=0.01,
>
> imin=1, ntx=1, ntpr=10,
>
> ntf=1, dielc=1, cut=12.0,
This is an awfully short cutoff for a non-periodic system. Consider
using one a bit bigger... like infinity (1000 is the same thing for most
systems).
>
> /
>
> &lmod
>
> xmin_method = 'PRCG'
>
> /
I think lmod is broken in sander and has been for some time (but don't
quote me on it).
If you want to use lmod, I would suggest the NAB implementation, which
has been working fine as far as I know. (There is a test case in
$AMBERHOME/AmberTools/test/nab that tests lmod and it should pass).
You can use that test case ($AMBERHOME/AmberTools/test/nab/tlmod.nab) as
a starting point for your calculation and just modify it as necessary.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 23 2014 - 07:30:02 PDT
