[AMBER] The output file about SMD

From: wjli <wenjuanli93.gmail.com>
Date: Sat, 9 May 2015 21:24:05 +0800

Dear Amber members,

I know SMD is quite complex and I am effectively a novice.

RST fle£º
&rst iat=507,503, r2=8.8, rk2=1.0725, r2a=5.8 /

I just dont understand what do the four columns of the output file mean:
15.00500 14.75768 2470.68119 3.07782
15.01000 15.13490 -1246.46571 6.13835
I guess x0 means the initial distance of the short time window£¬x is the final distance£¬the force is the mean force of the short time window£¬but the work is of the entire process£¿What about the plus or minus of the force£¨the direction is from residue 507 to 503)?

If I want just move residue 507(it is an ion ),what should I do ?Fix the whole protein ?

I simply want to know whether the ion can go through the tunnel and reach the active
site.I will very appreciate if anyone can offer more details about SMD using AMBER or related papers.

Look forward to your reply!
Best wishes.
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Received on Sat May 09 2015 - 06:30:02 PDT
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