<div dir="ltr">Hi,<div><br></div><div>Can you use the generated .mdp files if you issue gmx grompp directly? Does subprocess.call(['cat', newmdp]) work as expected?</div><div><br></div><div>Mark</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Nov 28, 2014 at 5:59 AM, Shirts, Michael R. (mrs5pt) <span dir="ltr"><<a href="mailto:mrs5pt@eservices.virginia.edu" target="_blank">mrs5pt@eservices.virginia.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi, all-<br>
<br>
I'm trying to write a python script using subprocess to call grompp. It<br>
works perfectly fine when called from the command line or when debugging;<br>
this only occurs with python (Anaconda, Python 2.7).<br>
<br>
For example, my code looks like:<br>
<br>
subprocess.call(['gmx_d','grompp','-f',newmdp,'-c',gro,'-p',top,'-o',tpr,'-<br>
maxwarn','5'])<br>
<br>
<br>
<br>
It produces to stdout:<br>
<br>
GROMACS: gmx grompp, VERSION 5.1-dev-20141126-f367cf6 (double precision)<br>
Executable: grompp<br>
Library dir:<br>
/Users/mrshirts/work/gromacs_allv/git/gromacs_official/install_gromacs_noit<br>
er/share/gromacs/top<br>
Command line:<br>
grompp -f r0000.noiter.mdp -c trpo.gro -p trpo.top -o r0000.noiter.tpr<br>
-maxwarn 5<br>
<br>
<br>
However, the errors that it then gives and mdout.mdp indicate that the mdp<br>
is not actually being read in, and the default values are being used<br>
instead. It even reports that the errors are in the mdp file I fed in,<br>
even though the mdp does not contain those commands.<br>
<br>
All files work perfectly well when called from the command line.<br>
<br>
The problems also occur the same way when calling as:<br>
<br>
subprocess.call(['grompp','-f',newmdp,'-c',gro,'-p',top,'-o',tpr,'-maxwarn'<br>
,'5'])<br>
<br>
So that's not the issue. Same thing happened with os.system.<br>
<br>
<br>
<br>
I've tried a bunch of different ways of calling it in python, and all fail<br>
to have the mdp read in. All other files are read in, and it doesn't<br>
matter what order they are in.<br>
<br>
I'm just wondering if other people have experienced this sort of problem<br>
calling gromacs with Python, or if there is something weird I'm doing.<br>
<br>
<br>
Best,<br>
~~~~~~~~~~~~<br>
Michael Shirts<br>
Associate Professor<br>
Department of Chemical Engineering<br>
University of Virginia<br>
<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a><br>
(434) 243-1821<br>
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