INCONSISTENCY messages and minimization in toturial 1-2-sphere

From: Yan Zhou (zhouyan_at_iupui.edu)
Date: Wed Sep 03 2014 - 03:14:30 CDT

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Dear All:

I am following the toturial to run the simulation of "1-2-sphere" in
namd-tutorial-files
with one cpu. The version is NAMD 2.9. I used the conf, pdb, psf and
parameter files provided in the tutorial. To make sure that I use the same
parameters as the ones shown in the standard log file in subfolder
"example-output",
i made some changes to "ubq_ws_eq.conf" as follow:
pairlistdist 14 -> pairlistdist 13.5
langevinDamping 1 -> langevinDamping 5

The value for "MIN ATOMS PER PATCH" in my output is 40, while it is 100 in
the standard log file, but I don't know how to adjust it.

I have two problems.
The first problem is the INCONSISTENCY messages:

Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000290274 AT 0.251946
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946

What is the reason for the presence of these messages and how they will
affect the simulation?
I couldn't find any useful information from the previous posts. I tried to
locate the source in the source files, but I also couldn't find it either.

The second problem is that the energies during the minimization in my
output are different from those in the standard log file.
For example, the energies of the unminimized configuration are the same in
these two output files:
my output:
ENERGY: 0 1947.9207 1238.5705 263.8635 10.7301 -18781.7697 1984.0070
71.1903 0.0000 0.0000 -13265.4876 0.0000 -13265.4876 -13265.4876 0.0000
standard output:
ENERGY: 0 1947.9207 1238.5705 263.8635 10.7301 -18781.7697 1984.0070
71.1903 0.0000 0.0000 -13265.4876 0.0000 -13265.4876 -13265.4876 0.0000

However, the energies in the subsequent minimization steps are different
between these two output files.
For example, the energies after the first minimization step:
my output:
ENERGY: 1 1948.9271 1238.1005 263.9798 10.9845 -18781.7618 1722.9304
71.1903 0.0000 0.0000 -13525.6491 0.0000 -13525.6491 -13525.6491 0.0000
standard output:
ENERGY: 1 1942.6174 1237.6136 263.8559 10.7135 -18782.3966 1967.2297
71.1841 0.0000 0.0000 -13289.1824 0.0000 -13289.1824 -13289.1824 0.0000

Aren't they supposed to be the same?

Thank you very much in advance!

Regards,

• Next message: Harris, Robert C.: "computing forces on atoms by postprocessing a dcd file generated with FEP enabled"
• Previous message: Akshay Bhatnagar: "Fwd: Reg: solvation in DMSO"
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