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There is no discussion of whether the MD simulations are reasonably equilibrated (5 ns is a short simulation using current software and hardware).  There is no critical assessment of whether the gaff force field correctly models the behavior of the substrates.
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The authors should demonstrate that their analysis is largely independent of the initialization process of this MD run by adding at least a second 5ns run,
initialized using different seed for random velocities.

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Óù½£½­ºþ(½ð±Ò+4): лл 2011-11-13 20:05:29
voleyes(½ð±Ò+2): 2011-11-16 00:08:21
voleyes(½ð±Ò+2): 2011-11-18 02:49:44
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voleyes

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5Â¥: Originally posted by kgyl at 2011-11-13 18:12:56:
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6Â¥2011-11-13 22:52:38
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kgyl

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6Â¥: Originally posted by voleyes at 2011-11-13 22:52:38:
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7Â¥2011-11-14 10:14:21
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xjping

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ghcacj(½ð±Ò+5): лл 2011-11-15 13:51:38
voleyes(½ð±Ò+4): 2011-11-16 00:08:42
There is no discussion of whether the MD simulations are reasonably equilibrated (5 ns is a short simulation using current software and hardware).  There is no critical assessment of whether the gaff force field correctly models the behavior of the substrates.
>>>>>>>>>>>>>>>>
First, you could list some references where GAFF FF can behave properly for substrate systems. The potential-time plot should help understand achievement of equilibrated.

ÁíÍâËû»¹ÒªÇóÔÙÖØÐÂ×öÒ»¶ÎÄ£Äâ
The authors should demonstrate that their analysis is largely independent of the initialization process of this MD run by adding at least a second 5ns run,
initialized using different seed for random velocities.
>>>>>>>>>>>>>>>>>>>>>>
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you could mention this in your text and let referee know you have demonstrate independence of initial configurations.
8Â¥2011-11-15 04:58:26
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