From: Sting (stg1979_at_emails.bjut.edu.cn)
Date: Tue May 31 2005 - 21:38:38 CDT
Thank you for suggestion.This system is a super-helix consisted of three chains,about 110 X 3 residues.I have performed a 10,000 steps minimization and 500ps MD(with CA fixed),then another 500ps free MD was performed.While minimization,the energy fluctuation(sorry,I shuld correct myself,that the changing energy is not VDW but Elect energy) didn't occur,but both the constrain MD and free MD presented the energy shift as said before.
By the way,during solvating the protein,we set the waters departing 3.3 Å from protein (defaut is 2.4 Å),and then did NTV MD. So that, at some specific positions near the protein, huge water holes occured.Did the Elect Energy shift has any relationship with this?
Thank you for your time.
======= 2006-06-01 02:12:52 ：=======
>May be you should better equilibrate the system before running MD.
>> When I performed a MD run with NAMD,every things went well,but when analyzing the energy of the system,I noticed that there was a large fluctuation between every two sequential steps,something like: step VDW energy
>> 259970 -226049.7557
>> 259980 -38243.0418
>> 259990 -226001.2423
>> 260000 -38106.4633
>> I wonder what I should understand this.
>> Any suggestion will be appreciated.
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