AMBER: Question about separating bonded force

From: Shawn yy <>
Date: Fri, 1 Jun 2007 10:31:04 -0500

Dear all,
   I met a strange problem when I tried to change the sander code. Since I
want to separate bonded force and nonbonded force in sander, I defined a
double precision array bfrc and passed this array instead of f (which
included nonbonded force already) to the subroutine bond, angle and ephi. So
all the bonded force were stored in bfrc. In order to obtain the total
force, I just simply add two array bfrc and f. However, this addition of two
force arrays gives me trouble. I have a testing system: a di-alanine
peptide solvated with 8 A buffer rectangular TIP3P box. I ran NPT
simulations using the modified sander and the original sander for 1000
steps. From the first step, there was already very small difference (1E-16)
between the total forces on some solute atoms obtained from two runs. The
differences increased gradually(1E-16 to 9E-16), but they were still found
on solute atoms only before step 55. After step 55, differences were also
found on many water molecules. After step 577, small differences on
nonbonded energies were found in output file (the two run had exactly the
same energy before step 577). The differences increased with time. At step
1000, output files of the two simulations were already very different. The
potential energy differed by around 9 kcal/mol. What could be the problem?
Is it induced by overflow/underflow when the bfrc and f array were added
together? What is the best way if I want to obtain bonded force?
   All my tests were executed on an Intel P4 workstation, RHEL 3.0, kernel
2.4.21-32.0.1.ELsmp, Intel fortran compiler 8.0, and Amber 9.

    Thank you very much for your help.

Lijiang Yang

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Received on Sun Jun 03 2007 - 06:07:37 PDT
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