GROMACS version: 2018.3
GROMACS modification: Yes/No
I have recently learned to perform coarse graining simulation on a protein using this martini tutorial: Proteins. After successfully performing all the steps using the sample files, I’m now trying to extend the production run to 2 microseconds. Usually in all atom MD simulation, I achieve that by tweaking the ‘nstlim’ in the production-input file. I tried to do the same here, in the ‘dynamic.mdp’ file I changed the nsteps to 70000000 (and dt=0.03ps), which should give me a simulation time of 2.1 microsecond. However, when I execute the production run using the ‘gmx mdrun -deffnm dynamic -v’ command, it still runs only for the default 3000000 steps. What am I doing wrong here?
Thanks for your help in advance.
nstlim is not a valid keyword, but nsteps is. If you need to extend an existing simulation, please follow Managing long simulations — GROMACS 2021 documentation
@jalemkul My apologies, I meant nsteps (nstlim is the keyword in all-atom MD).
Thank you @jalemkul sir. In the link that you shared, it says: The time can also be extended using the -until and -nsteps options. Can you kindly elaborate how to achieve that? As I mentioned above, I tried changing the value for -nsteps, but it didn’t work.
Please provide the exact sequence of commands you used. You need to create the new .tpr file with one of the convert-tpr options, then use mdrun -cpi -append with the new .tpr and previous .cpt file.
Hi @jalemkul
First I ran the command: gmx convert-tpr -s dynamic.tpr -extend 67000000 -o dynamic_extended.tpr which ran without any issues.
Then,
I ran this command: gmx mdrun -s dynamic_extended.tpr -cpi dynamic_prev.cpt
But, it gave me the following error:
Command line:
gmx mdrun -s dynamic_extended.tpr -cpi dynamic_prev.cpt
Output file appending has been requested, but some output files listed in the checkpoint file dynamic_prev.cpt are not present or not named as the output files by the current program:
Expect output files present:
Expected output files not present or named differently:
dynamic.log
dynamic.xtc
dynamic.edr
Program: gmx mdrun, version 2018.2
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 179)
Fatal error:
File appending requested, but 3 of the 3 output files are not present or are
named differently. For safety reasons, GROMACS-2016 and later only allows file
appending to be used when all files have the same names as they had in the
original run. Checkpointing is merely intended for plain continuation of runs.
For safety reasons you must specify all file names (e.g. with -deffnm), and
all these files must match the names used in the run prior to checkpointing
since we will append to them by default. If you used -deffnm and the files
listed above as not present are in fact present, try explicitly specifying
them in respective mdrun options. If the files are not available, you can add
the -noappend flag to mdrun and write separate new parts. For mere
concatenation of files, you should use the gmx trjcat tool instead.
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs