AMBER Archive (2006)

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

From: thanyarat Udom (thanyarat22_at_yahoo.com)
Date: Tue Mar 07 2006 - 01:17:23 CST

Dear All
   
              Thank you for your suggestion, This problem has been solved.

   
                                                                          Best Regard

                                                              Thanyarat Udommaneethanakit

  
Ross Walker <ross_at_rosswalker.co.uk> wrote:
      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
  Ross
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---------------------------------
  From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of thanyarat Udom
Sent: Monday, March 06, 2006 00:52
To: amber_at_scripps.edu
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 follows.
  cut off Total Energy(NSTEP=1) BOND ANGLE DIHED VDWAALS EEL
    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 Å look very strange. The minimization has not been employed PBC (ntb =0). Please help me.
                                                               Best Regard
                                                    Thanyarat Udommaneethanakit

    
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