Getting this error : gmx_mpi': corrupted size vs. prev_size: 0x0000000001d1b320 ***?

Manoj Rana @Manoj-Rana-10

18 July 2024 1 6K Report

i am using the trjconv command in gromacs

gmx_mpi -debug trjconv -s md.gro -f md.xtc -o utr.xtc -fit rot+trans

and after few steps i got the error

gmx_mpi': corrupted size vs. prev_size: 0x0000000001d1b320 ***

if anyone know how to resolve it , I will be gratefull

thanks you

Ricardo J Ferreira

It means your trajectory file is (probably) corrupted. Try start reading it after the number of steps in which it gives error(if it gives error at step 10, try -b 20)

Badges
Science topic

Similar topics
Filing

More Manoj Rana's questions See All

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

How to remove the residual PDMS on the silicon mold?

Incompletely cross-linked pdms are difficult to remove.

01 March 2021 798 3 View

Can anyone provide the Support vector regression code structure of LIBSVM MATLAB or python ?

Please, if Gaussian Parameter optimization is possible in this code structure

28 February 2021 278 3 View

What are the important topics in the field of Artificial Intelligence in Business world?

Dear All, I am doing my MS in Electronic Businesses. And I am interested in the AI field and its applications for businesses, its benefits, impacts, etc. What kind of scientific research dominate...

26 February 2021 8,816 6 View

Why CNN algorithm performs well in Network Intrusion Detection based on some recent resources?

Most of the papers have compared different hyperparameters such as layers, initializers, activation function, and optimizer algorithm in the CNN algorithm for detecting network intrusion. This is...

24 February 2021 4,578 4 View

Is there any solar electric power plant having the concentrated photovoltaic modules?

The solar photovoltaic (PV) power plant uses commercial (non-concentrated) PV modules which are quite simple in design and reliable. They can work on fixed orientation and don't need the moving...

16 February 2021 3,796 9 View

Do anyone have a full MATLAB code for structural topology optimization using Genetic Algorithm? Such as a cantilever beam?

Do anyone have a full MATLAB code for structural topology optimization using Genetic Algorithm? Such as a cantilever beam? Could you provide some MATLAB code to me , a beginner for GA. Thank...

03 February 2021 3,789 5 View

How is it possible to rank variables using Likert scale?

Hello Everyone, I have a questionnaire of a 3-point Likert scale for an overall evaluation for a service, and several detailed attributes evaluation of that service. For example: Overall...

31 January 2021 9,612 8 View

How to extract peaklists from mass spectrometry raw file and do mascot search for my protein in ncbi?

I have a raw file of tandem mass spectrometry (LC-MS/MS) data. I want do online protein databank search for my protein identification and its homology.

30 January 2021 3,081 3 View

Can anyone provide me with the scoring method and the questionnaire of Work life balance scale by Hayman (2005)?

Greeting! For my MA dissertation, I am thinking of taking Work life balance scale by Hayman. However, I can't find the scoring procedure; also confused about the actual rating taken. If anyone...

23 January 2021 4,074 7 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Timeout error!! Processor in the loop (PIL) using STM32F4 Matlab 2018a?

Dear Researchers I am trying to perform a PIL simulation using STM32F4 Discovery board and comunication serial USB TO TTL. During simulation I receive the following timeout error: An error...

01 March 2021 2,327 1 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

Difficulty in debugging code to correct error - TypeError: '<' not supported ?

I am trying with a Unet code ontained from net ...in tensorflow. When trying to predict the segmentation result with the trained and saved model with metric " iou" using "CustomObjectScope"...

22 February 2021 5,254 1 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Problem in energy minimization using Gromacs?

I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.

18 February 2021 4,822 2 View