Re: [AMBER] minimization/equilibration amber 12 - wont generate .mdcrd and .ene files

From: Amparo Garcia Lopez <Amparo.GarciaLopez.unige.ch> Date: Thu, 14 Nov 2013 12:54:20 +0000

---
From: Jason Swails [jason.swails.gmail.com]
Sent: 14 November 2013 13:38
To: amber.ambermd.org
Subject: Re: [AMBER] minimization/equilibration amber 12 - wont generate .mdcrd and .ene files
On Thu, 2013-11-14 at 12:16 +0000, Amparo Garcia Lopez wrote:
> Dear all,
>
> we have been trying to run a minimization followed by equilibration in amber12. We have tried both pmend and sander, and with both we have the following problem.
>
> We use these options
>
> mpirun -np 4  $AMBERHOME/bin/sander.MPI -O -i md8.in -o md8.out -p md.top -c md7.crd -ref md7.crd -r md8.rst -x  md8.mdrcd -e md8.ene &
>
> the program will not generate the trajectory file (-x option) nor the energies file (-e option). However, the program does generate the .rst (-r) and .out (-o) files. We have tried with two different molecules, and the same thing happens, so it's not the system.
sander and pmemd do not automatically write trajectories and energy
files.  To write a trajectory file, you must set ntwx>0 in the &cntrl
section of the input file. The default value of ntwx is 0, so unless you
set it in the input file no trajectory will be written.
Likewise for the mdene file, you need to use the ntwe variable in the
&cntrl section of the input file and set that to a non-zero value.  The
manual has more details about these variables.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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