[gmx-users] Using a 4.6.5 cpt file in 5.0 to extend a run?

Mark Abraham mark.j.abraham at gmail.com
Thu Sep 25 09:55:04 CEST 2014

On Thu, Sep 25, 2014 at 5:03 AM, Nathan Scott <scottjn at gmail.com> wrote:

> Hi all,
> I am trying to extend some simulations done on the XSEDE Trestles system
> over the summer, and they have upgraded to 5.0 since then from 4.6.5.

That's not normal practice at compute centers - older versions should
generally continue to be made available, so that a scientific project can
have a consistent methodology. In principle, a trajectory could be
continued with newer software if it implements the same method, but proving
that this principle holds is more trouble than you should normally want to

Can anyone give any tips for navigating around the below error?
> Program mdrun_mpi, VERSION 5.0
> Source code file:
> /state/partition1/git/chemistry-roll/BUILD/gromacs_intel_mvapich2_ib-5.0/gromacs-5.0/src/gromacs/gmxlib/checkpoint.c,
> line: 2037
> Fatal error:
> You seem to have switched ensemble, integrator, T and/or P-coupling
> algorithm between the cpt and tpr file. The recommended way of doing this
> is passing the cpt file to grompp (with option -t) instead of to mdrun. If
> you know what you are doing, you can override this error by setting the
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> In fact, I haven't switched any of the mdp options that were used for the
> original simulation, except nsteps, and doing a diff of the mdp file the
> original cpt file is based off of and the new one that I am trying to use
> to extend the simulation confirms this fact.

OK, but sometimes the internal representation has to change, as it did for
(say) the new implementation of the default sd integrator, or the default
for cutoff-scheme. Depending what the actual issue is here, maybe the error
message could use improvement.

Is there a workaround for this?

Like the message says, you can do
 grompp -f new -c whatever -p topol -t the-4.6.5.cpt

 in order that your intentions are explicit. mdrun should have logic to
stop you doing things that likely are mistakes, such as

 mdrun -s nvt -cpi npt

but we can't write code that anticipates all possible scenarios and reacts
the way every user would expect...

Or might I just be making some kind of
> simple mistake? Any advice would be greatly appreciated!
> Best Wishes,
> Nathan
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