From: sunita gupta (sunita.bio_at_gmail.com)
Date: Fri Jan 02 2009 - 03:58:37 CST
Hi all,
I am doing the coarse grain simulation of a protein around 600 residues.
After minimization when I am heating my system I am encountering an error
*"ERROR: Atom 3430 velocity is 3106.47 2328.51 -12.5113 (limit is 1000)
ERROR: Atom 3548 velocity is 479.695 -98.743 -1895.5 (limit is 1000)
ERROR: Atom 3782 velocity is -862.237 451.473 -232.745 (limit is 1000)
ERROR: Atom 3932 velocity is 10558.1 -3567.96 2505.98 (limit is 1000)
ERROR: Atom 4326 velocity is 2550.07 35.6837 1606.01 (limit is 1000)
ERROR: Atom 4393 velocity is -74.071 -1839.18 713.27 (limit is 1000)
ERROR: Atom 4402 velocity is 91.7628 1845.16 -693.08 (limit is 1000)
ERROR: Atom 5824 velocity is -10546.3 3561.58 -2532.62 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 7955 velocity is -215.633 -1008.42 -1042.81 (limit is 1000)
ERROR: Atom 8252 velocity is 396.536 2473.09 152.247 (limit is 1000)
ERROR: Atom 8345 velocity is 949.577 519.289 -570.563 (limit is 1000)
ERROR: Atom 8376 velocity is -944.965 -504.078 573.664 (limit is 1000)
ERROR: Atom 8852 velocity is 71.9893 1061.93 965.823 (limit is 1000)
ERROR: Atom 8904 velocity is -506.517 109.389 -923.522 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely."
*
After going through the mailing list I found that its due to not enough
minimization, so I have minimized it lastly to 20000 steps, but after that
again I am facing this problem.
One more thing that I am observing is that the value of GRADIENT TOLERANCE
is also very high (fluctuating around 40 and never going below 1).
Can anyone suggest the cure to this problem. Any help will be highly
appreciated.
Thanks and Regards
-- SUNITA GUPTA
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