Reg: movement of protein outside box

From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Mon Jun 09 2014 - 20:46:56 CDT

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Hello everyone

I have performed a 10 ns equilibration to simulate a amino acid in a 30 A
water box, but after the equilibration the amino acid has moved to the
corner of the box. can anyone explain me the reason?

Also can anyone tell me the exact difference between equilibration and
production run? If I use pressure control parameter in equilibration then
is it equivalent to production run?

Thank you very much

With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus

• Next message: Aron Broom: "Re: Reg: movement of protein outside box"
• Previous message: Shailesh Pandey: "NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation??"
• Next in thread: Aron Broom: "Re: Reg: movement of protein outside box"
• Reply: Aron Broom: "Re: Reg: movement of protein outside box"
• Reply: Norman Geist: "AW: Reg: movement of protein outside box"
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