Re: [AMBER] Atom Expression in NAB

From: Jason Swails <>
Date: Mon, 9 Dec 2013 07:08:20 -0500

On Mon, Dec 9, 2013 at 12:21 AM, sunita gupta <> wrote:

> My another concern is to change the cut-off parameter from 100(default) to
> 12 A while minimization using minab.
> I copied minab.c and file into my local directory and changed the
> values, but could not succeed.
> Somewhere I read about recompilation...dont know how to do it.

minab.c is a temporary file -- it is not useful to you. To compile nab
programs, you need to use "nab" as the compiler. In this somewhat simple
case, you would use the command:


This will create a temporary (not useful) minab.c file as well as a program
named a.out. You can run this a.out program:


> Also, I want

> to know abo
> ut MPI implementation in NAB .

it parallelizes some features of NAB. The MPI nab compiler is "mpinab"
instead of "nab" (much like mpicc and mpif90 instead of the C compiler and
Fortran 90 compiler). Just use "mpinab" instead of "nab":


You can then use "mpirun" to run multiple threads of this new program:

mpirun -np 8 ./a.out

A (better) alternative to parallelizing NAB programs is to use OpenMP. You
would need to configure with the -openmp flag. Note that OpenMP and MPI
are considered advanced options, especially for NAB, so you will need to
experiment a bit to work out the best way to run in parallel on your
system. A couple comments: not every part of NAB is parallelized (like the
normal mode part, to my knowledge). Unless you plan on doing
time-intensive tasks (like implicit solvent dynamics or long
minimizations), it is probably better to just use serial nab.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 09 2013 - 04:30:02 PST
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