Seeking help about GROMACS 5.1.2 error "File input/output error: Cannot write trajectory frame; maybe you are out of disk space?

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Does diseases like fungal,bacterial etc of rice plant is different from nutrient deficiency diseases?how deep learning is used except classification?

can any one suggest me other than classification, how deep learning technique can be used in plant disease detection in rice plant? could a research work continued from fungal,bacterial...

07 February 2021 470 2 View

Without using a course aggregate why the topic is named as Textile Reinforced Concrete? & why not it is named as Textile Reinforced Mortar Cement?

Dear Researchers, In Textile Reinforced Concrete is a novel construction material consisting of a cementitious binder and a textile reinforcement. Without using a course aggregate why the topic...

24 January 2021 2,654 9 View

What is the use of vaccination without follow-up tests for assessing the corresponding antibodies ?

Shouldn't every individual who takes COVID-19 vaccination undergo periodic review to the study the state of corresponding antibodies? Individuals who do not produce any symptoms of COVID-19 after...

23 January 2021 6,170 2 View

In a xrd pattern how to check if any of the peak is due to presence of super lattice(SL)? Any conditions to check & confirm SL peaks?

I have a xrd pattern, in that i suspect that one of the peak may be due to SL, i want to understand how to confirm it or reject it

07 January 2021 5,534 3 View

What etchant should be used for Annealed 17-4 PH stainless steel sheet ??

I wish to determine microstructure of 17-4 PH stainelss steel sheet (annealed condition). What etchant should I use so that a clear microstructure can be found out ??

03 January 2021 9,836 2 View

What is the difference between PEEQ, PE and LE options in abaqus ??

I wish to find out thickness variation in my model, so for that which one I should choose among PEEQ, PE and LE ??

26 December 2020 6,542 2 View

Do you think selfishness and opportunism are key to the success?

Do you think selfishness and opportunism are key to the success? Dou you agree that principles, morals, ethics, intelligence etc. are only useless, show-words, even in the fields of science,...

24 December 2020 10,015 12 View

List of scopus/ DOAJ indexed medical education journals?

suggest some indexed journals with low publication charges that publish medical education related research projects

22 December 2020 6,909 3 View

Hi, What is the basic difference between an ultramer and a gblock?

I am planning to overexpress an sRNA in K.pneumoniae (inherently resistant to Amp, hence cannot use pUC19 because of it Amp resistance and not useful to scree). Which is better to clone in an...

14 November 2020 1,530 3 View

How to plot thickness contour plot and load diaplacement diagram in stretching simulation in abaqus ?

How can we plot thickness contour plot in stretching simulations in abaqus. Thickness contour plot means variation of thickness with time as stretching takes place. How can we plot load Vs...

10 November 2020 1,019 3 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

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

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

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 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

RDF calculation of water inside the Carbon nanotubes?

I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...

17 February 2021 1,066 3 View

Indu Kumari

Check the disk space, there is not enough space in the disk in which you are running MD simulations. Move some data (Not required for running this simulation) from your disk to other disk in which space is available.

Harikrishna Reddy R

I have 65GB of free space on disk, from MD it is about to generate 2583MB data.

Sotiris Papadatos

Probably this has nothing to do with actual disk space. Could you please give us some more information. Like system size, on which command this error occurs? etc (Of course information that you are able to give)