[gmx-users] Protein-surface interaction during flow

Smith, Micholas D. smithmd at ornl.gov
Tue Jan 31 14:25:01 CET 2017

Hi Mark,

The gro file will not store the velocities, but a *.trr file will (for all frames, provided you set velocities to be saved in your mdp file). The cpt files will only have the velocities for the last step that was check-pointed. Your command is correct though otherwise. If you want to get velocities from a frame other than the last one you will need to record that frame to a file (gmx trjconv can be used for this) and read it into grompp with the -t flag.

But yeah, the command gmx grompp -f new.mdp -c last_frame.gro -o new.tpr -t old.cpt will give you a "new" simulation with the velocities your "new" initial velocities.

Happy Simulating.


Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kamps, M. <m.kamps at student.rug.nl>
Sent: Tuesday, January 31, 2017 4:27 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Protein-surface interaction during flow

Dear Micholas,

Thanks for your reply and suggestions!

Your idea at point 2, how can I do this? The forces and velocities are
stored in the .edr files, while the final velocities and positions are
also stored in the output .gro file right? This means I should run a
simulation just long enough that the proteins reach a desired point,
after which I can use the final .gro  or the .edr files?
I then need to continue (extend) my simulation, while creating a new
.tpr file via the new .mdp file, effectively using this command:

gmx grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt
mdrun -s new.tpr

Will this continue my simulation with the 'previous' velocities? Since
none of these files will input any .edr or .gro files?

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