AMBER Archive (2005)

Subject: Re: AMBER: Is the MD simulation normal

From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Sun May 29 2005 - 09:53:35 CDT

Dear Prof. Ross,

Seeing form the plot of RMSD as a function of time, it take 300 ps or
so to reach the equibilbration. I think there may exists problems.

I will perform two MD as the control.

First, I think I can use amber7 to perform One MD that was earlier
performed ok. The reason that I paln to perform this MD is that, When
using amber7, I have meet no problem with the MD.

Second, about this MD that we disscussed, I will use constraint NPT MD
for the first 300 ps and with a following 1 ns NPT MD without
constraints. If the result generated in this MD is similar to the
original results, it indicates that the disscussed MD results are
completely right.

What is your advice.

By the way, thanks for many experts to help me disscuss the MD!

Best regards.

shulin 

-- 
   Shulin Zhuang
Chemistry Department 
Zhejiang University PRC
shulin.zhuang_at_gmail.com
  • application/msword attachment: RMSD.doc
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