Re: [AMBER] NFE error: Cannot read &abmd namelist

From: Feng Pan <>
Date: Tue, 2 Apr 2019 19:56:47 -0400

Hello, Jason

I got your files and do some test runs. And found a couple of issues.

-For the 2D CV, the cv_ni should be 110 instead of 88, since the zeros will
also be counted.
-in the mdin files, set monitor_freq=2500, not monitor_freq=`2500`, get rid
of the single quotes, the
  variable should be integers instead strings
-change the ntwv to 0 in mdin files, which will lead to errors, actually
this can be easily fixed,
  if you really need the velocity trajectory, send me an email and I will
send you the fixed one.

After correcting those, I did tests on both 1D and 2D CVs with 2 groups, no
problem. I assume
there should not be any problem if you extend to 16 groups.


On Mon, Apr 1, 2019 at 3:55 AM Jason Imamoto <>

> Hello Users,
> I have tried the modification made by Feng Pan. Unfortunately, the error
> still occurred. I believe this is due to the way my collective variable
> (CV) file is setup.
> I have attached all the files that I use to run the program. There are
> two cv_NoB_mRMSD_ALin1*.in files. The copy version contains both CVs that
> I want to use. The other version only contains the Number of Bonds (NoB)
> CV. I tried to problem solve with the NoB CV, but it still produced the
> same error. The creates the cntl files from the
> samp_2D_Lin1_Aform.cntl.
> Due to the size of the restart file, I did not include it. If you would
> like it to test my *.in files, I will gladly provide the restart file.
> I appreciate any and all suggestions.
> Thank you for your time and help.
> 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:
> _______________________________________________
> AMBER mailing list

Feng Pan
North Carolina State University
Department of Physics
AMBER mailing list
Received on Tue Apr 02 2019 - 17:00:03 PDT
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