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