AMBER Archive (2004)

Subject: AMBER: how to calculate E-pot from restart file?

From: J. Zhang, Dr (jzhang_at_biophy.nju.edu.cn)
Date: Thu Jul 08 2004 - 22:13:44 CDT

Dear amber users,

I did a MD calculation with this mdin file
----------
imin=0,ntpr=1,ntwr=1,ntwx=1,ntwe=1,nstlim=1,
..
----------
then I got a restart file md.rst and the
corresponding E-pot=-200 from the md.out file.

now my question is, if I only have the md.rst
file, how to calcuate the corresponding E-pot.

my method is to do a 1-step MD again with this
restart file, but the obtained E-pot from md.out
is E-pot=-207, which is not equal to the value
of previous run. This is due to rounding error?
how to get the exact E-pot from only the restart
file?

I am sorry for this simple question.

Best Regards,
J. Zhang, Dr
Institute of Biophysics
Nanjing University

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu