RE: AMBER: the total energy is not converge as the cutoff increase

From: Ross Walker <>
Date: Mon, 6 Mar 2006 07:39:51 -0800

Hi Thanyarat,
What you are seeing is to be expected. You are not using periodic boundaries
and I assume are doing a gas phase simulation without a dielectric or any
implicit solvent treatment. Then what you are seeing is correct.
Electrostatic interactions in gas phase are extremely long range. So long
range in fact that I would argue that you cannot justify the use of a cutoff
with a gas phase simulation.
Why do you want to simulate your system in gas phase? If you do an explicit
solvent calculation with PME you should see the electrostatic energy
converge around 8 angstroms as these types of calculations include the full
infinite electrostatic interactions via a combination of real and reciprocal
space sums.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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From: [] On Behalf Of
thanyarat Udom
Sent: Monday, March 06, 2006 00:52
Subject: AMBER: the total energy is not converge as the cutoff increase

Dear Amber users
          I want to run an energy minimization of protein/water/counter ions
system. First, I have tested cutoff the value of non-bonded. I summarized
the output from the first step (NSTEP = 1) of energy minimization as
cut off Total Energy(NSTEP=1) BOND ANGLE DIHED
  10 -145910 2629.283 5045.8942 10443.8164
30238.3127 -243907.946
 12 -262380 2629.283 5045.8942 10443.8164
29518.1267 -356388.753
 15 -302340 2629.283 5045.8942 10443.8164
29052.2034 -395395.948
 18 -260040 2629.283 5045.8942 10443.8164
28855.7353 -355521.277
 20 -571410 2629.283 5045.8942 10443.8164
28731.883 -667743.075

 Surprisingly, the total energy is not converge as the cutoff increase.
Particularly, the results at cutoff = 20 look very strange. The
minimization has not been employed PBC (ntb =0). Please help me.

                                                             Best Regard



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Received on Sun Mar 12 2006 - 06:10:08 PST
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