[gmx-users] Running Grompp in reverse and backing up MD data

Justin Lemkul jalemkul at vt.edu
Thu Nov 29 15:14:48 CET 2018

On 11/29/18 6:43 AM, Peter Kroon wrote:
> Hi Mark,
> thanks for the rapid reply!
> Hmmn. It doesn't have to be exactly matching input. An equivalent to
> e.g. mdout.mdp produced by grompp would already be good enough for my

All of the input .mdp settings are also written to the header of the 
.log file for the run.


> purposes. The same goes for a top file containing only the interactions
> relevant to the system.
> Peter
> On 29-11-18 11:31, Mark Abraham wrote:
>> Hi,
>> Unfortunately there is no way to generate matching inputs to grompp from a
>> .tpr file. In the longer term, we want that to be possible, but it will
>> require a total rework of how users specify inputs, and that's a large
>> effort!
>> Mark
>> On Thu, Nov 29, 2018 at 11:27 AM Peter Kroon <p.c.kroon at rug.nl> wrote:
>>> Hi all,
>>> In the lab we're thinking about backup solutions for MD data (and in
>>> particular gromacs produced data). Since trajectories tend to be large
>>> we quickly decided that backing up the results of simulations is a waste
>>> of disk space. Instead, we'll probably go for backing up the TPR files.
>>> Now for the question: Is there an easy way of generating the files used
>>> to generate the TPR files? For example the MDP file used to make a TPR
>>> file? How about a top file (I assume the original split between top and
>>> itp is lost)? I know I can get the starting configuration (gro) using
>>> editconf.
>>> And does anyone here have any other blinding insights on backing up MD
>>> data?
>>> Cheers,
>>> Peter
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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