[gmx-users] QUERY IN GRO FILE

Peter Stern peter.stern at weizmann.ac.il
Thu Mar 30 11:20:34 CEST 2017

Those are not two different commands, rather the same command with different options.
If you are not familiar with the options of the command, then

mdrun -h

will list them for you.  Specifically, in the second instance of mdrun you get the default output file name confout.gro whereas in the first instance you have changed all the output files to be em.sometype.


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Neha Gupta
Sent: Thursday, March 30, 2017 8:53 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] QUERY IN GRO FILE

Hi gromacs users,

I have a doubt in this command,

grompp -f em.mdp -c conf.gro -p topol.top -o em

mdrun -v -deffnm em

These commands generate em.gro, em.tpr, em.trr, em.log file.

There is another command which is

mdrun -s em.tpr

which generates confout.gro

Does em.gro and confout.gro are one and the same?

What are the technical differences?


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