AMBER Archive (2006)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Mar 06 2006 - 07:28:04 CST

Hi thanyarat,
   
  What would you need such a long-distance cutoff (cut=20) for your initial minimization step (imin=1, ntb=0)? Why don't you try cut=10 for your minimization, then turn on your periodicity (ntb=1) and make sure that your cut value is a little less than half the size of your peridic box. You can get the periodic box info from your leap.log.
   
  regards,
   
  jenk.

thanyarat Udom <thanyarat22_at_yahoo.com> wrote:
    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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