Hi, Jason
I am not sure if it the ABMD method that caused the problem. Please try
again without the ncsu_abmd block. Also can you send me the prmtop and
inpcrd file. I can run to test for you.
Best
Feng Pan
On Fri, May 27, 2016 at 1:20 PM, Jason Imamoto <jimamoto.mail.usciences.edu>
wrote:
> 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 - 13:30:02 PDT
