AMBER Archive (2008)

Subject: RE: AMBER: NAB to calcuate entropy. .

From: Wang, Xuelin (Xuelin.Wang_at_STJUDE.ORG)
Date: Wed Feb 20 2008 - 18:14:01 CST

Dr Case,

I figured out the problem I posted before in my first email. The answer is I didn't define the x[] right, which should be 3*the number of atoms. Then I used the revised input to do testing with a small DNA molecule. It works (see the last email I sent you). However, when I used the same input to test a larger system, there is a new error:

"allocation failure in vector: nh = -4617656057229413269"

I attached all input and output for your reference. I guess there is some memory allocation issue. If any way to solve it, let me know.

Thanks
Xuelin

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of David A. Case
Sent: Wednesday, February 20, 2008 5:19 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: NAB to calcuate entropy. .

On Wed, Feb 20, 2008, Wang, Xuelin wrote:
>
> Here are the output, input pdb file and nab input file. I used a small
> DNA molecule to do testing. It works without using nsnb=99999. Is it
> right?

Now I am confused...when does it fail? Did the files you sent show a failure?
Can you reproducibly change only nsnb and go from "good" to "bad" results?
Please only send files that show a problem.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu




-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu