[gmx-users] Averages are not printed in log files after changing the .mdp files during HREMD restart

Shyno Mathew sm3334 at columbia.edu
Fri Feb 26 23:28:24 CET 2016

Dear all,

I am running a long HREMD in multiple steps, each simulation is 5ns. I have
accumulated data for 40ns, till this point I was restarting the simulation
from the previous step without any changes. After 40ns, I decided to reduce
the size of .trr files, so I changed the .mdp files. Here is what I did
similar to the changing .mdp options discussed here

1. Created new mdp files for each replica. In the mdp file I increased the
nstxout, nstvout

2. Then created new .tpr files using new .mdp files
grompp_mpi -f ./mdout0.mdp -c ./8topol0.tpr -n ./sep.ndx -p ./topol0.top -o
./topol0.tpr -t topol0.cpt >& 9topoltpr0.log

3. Restarted the simulation
mpirun -np 96 mdrun_mpi -v -deffnm topol -cpi topol -plumed plumed.dat
-multi 32 -replex 1000 -nsteps 2500000 -hrex

*The simulations is running ok, exchanges are happening. However the
averages are not printed at the end of log files as it was doing before. So
I can't see the empirical transition matrix.*

Not sure how to fix this.

thanks in advance for your help,

Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University

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