[AMBER] Adaptively Biased MD: Problems with executing groupfile

From: Jason Imamoto <jimamoto.mail.usciences.edu>
Date: Fri, 27 May 2016 13:20:07 -0400

Dear Amber Users,

I have been performing adaptively biased (AB) MD simulations using Amber 14 to simulate an RNA structure. For some reason the ABMD simulations are failing on one computer, but running on another computer that is setup in the same fashion. The error states that the mdin (control) file cannot be read or is missing. This indicates that the program is not able to execute the groupfile and open the control file. I am not sure as to what is causing these failures. Therefore any and all help to fix this issue will be appreciated. Attached is the groupfile, PBS file, control file, and error file. The restart file could not be attached to the file due to the file size limitation, but if you would like the file(s) I can email them. The files listed are simplified to simulate only two walkers, but in reality 16 walkers are simulated. Pasted at the end of the email are the last few lines of the outfile. If more information is needed please let me know.

I look forward to your response.

Jason M. Imamoto
Doctoral Candidate
Department of Chemistry and Biochemistry
GH 302
University of the Sciences in Philadelphia
600 S 43rd St. Philadelphia, PA 19104

Email: jimamoto.mail.usciences.edu

Last few lines of the outfile:

 Number of triangulated 3-point waters found: 11000
| Atom division among processors:
| 0 4198 8392 12589 16786 20980 25177 29374
| 33568

     Sum of charges from parm topology file = -10.50000001
     Assuming uniform neutralizing plasma
| Running AMBER/MPI version on 8 nodes

| MULTISANDER: 2 groups. 8 processors out of 16 total.

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Received on Fri May 27 2016 - 10:30:02 PDT
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