REMD: "topol.tpr" required but I do not have it

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1

GROMACS version:2019
GROMACS modification: No
Here post your question

I am running REMD. I use the protocol of Justin’s lysozyme to prepare all the EM/NVT/NPT at different temperature folders, and generate individual md_0_1.tpr files.

Then I use command

gerun mdrun_mpi -v -multidir 1_338.15 2_339.2 3_340.26 4_341.31 5_342.37 6_343.44 7_344.5 8_345.57 9_346.64 10_347.72 11_348.79 12_349.87 13_350.95 14_352.04 15_353.12 16_353.15 -replex 100

to run the REMD, but was told

File input/output error:
topol.tpr

But topol.tpr files are not generated during the EM/NVT/NPT steps.

Also, which files are required to run the REMD? For a normal MD, only the tpr file is required.

2

Hi,
the problem is that mdrun do not find the tpr files. The option -multidir requires that you provide a set of n directories for the n simulations, place all the relevant input files in those directories (e.g. named topol.tpr )
see more Useful mdrun features — GROMACS 2020.5 documentation

Best regards
Alessandra

3

Hi Alessandra, thank you! I do have a md_0_1.tpr file in each temperature folder. It is just does not have the name of topol.tpr. Does it mean I just need to change the names of all the md_0_1.tpr into topol.tpr?

How do I know the name of the tpr file should be topol.tpr?

What other files are needed? I have already prepared multiple temperature folders, and copied each tpr file to each folder.

4

You didn’t specify any file names in your command, so mdrun looked for the default input to -s, which is topol.tpr. You can use any file names you like as long as you actually specify them, via -s or -deffnm.

5

I see, thanks.

Do I also need to supply -cpi -append ? I am running it on our cluster, so I want to request less computational resources. But I want to submit -hold_jid jobs to continue from the previous check point.

e.g.
gerun mdrun_mpi -v -deffnm md_0_1 -replex 100 -cpi -append -multidir 1_338.15 2_339.2 3_340.26 4_341.31 5_342.37 6_343.44 7_344.5 8_345.57 9_346.64 10_347.72 11_348.79 12_349.87 13_350.95 14_352.04 15_353.12 16_353.15

6

All relevant mdrun options still need to be provided. Your command simply tells mdrun there are multiple simulations to be performed in the listed directories, but provides nothing else. If you are doing a continuation, you need to add those options.

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