[gmx-users] tpr format

Mark Abraham mark.j.abraham at gmail.com
Wed Feb 27 19:09:13 CET 2013

On Wed, Feb 27, 2013 at 1:21 PM, 何斌 <binhe at hustunique.com> wrote:

> hi,
>     everyone.
>     I want to konw that if there is any difference between the tpr files
> generated by gromacs4.6 and the older version gromacs,such as gromacs3x。

Yes. We do work hard to make sure that new code can run old .tpr files to
the extent that the old features can be implemented by the new code.

       When I run myrun ,the error is:
> Back Off! I just backed up 1.2.log to ./#1.2.log.2#
> Reading file gmx_workload2.tpr, VERSION 4.0 (single precision)
> Note: file tpx version 58, software tpx version 83
> Converting input file with group cut-off scheme to the Verlet cut-off
> scheme
> Converting switched or shifted interactions to a shifted potential
> (without force shift), this will lead to slightly different interaction
> potentials
> ------------------------------**-------------------------
> Program mdrun, VERSION 4.6
> Source code file: /home/shwzhou/gromacs/gromacs-**4.6/src/kernel/runner.c,
> line: 741
> Fatal error:
> Will not convert old tpr files to the Verlet cut-off scheme with
> free-energy calculations or implicit solvent
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
> ------------------------------**-------------------------
> so ,if you can tell me how to solve this problem and the reason for this
> problem?

Don't trigger the use of the Verlet kernels. Since you've not told us what
this simulation should be doing or how you're calling mdrun, you're making
everyone's life hard.

> ps:I only have the tpr file ,so it is impossible to generate it use the
> new version gromacs.

Well, you won't be able to use the Verlet kernels in combination with
whatever this old .tpr did. Your best course of action is likely to be to
get the old mdrun, look at the start of the .log file to see what it was
doing, compare that to what you can get from gmxdump and build a new set of
input files for grompp.


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