How to run GROMACS on cluster?

More Shradheya Raj Rajeshwar Gupta's questions See All

What are the most reliable approaches to extract key continuous frames from a video, with complete automation?

I have an input video, of skin (from a microscope that means it is magnified such that blood capillaries are visible). The idea is to extract 15 sec of continuous frames from a video of 1 min,...

02 March 2021 2,735 2 View

Which microtomy technique do you suggest for thin and delicate root sectioning ?And, how to preserve and process the roots before sectioning?

We have thin roots of from 1 year old different species of plants. We are looking into anatomical details of the roots. What's the best method to preserve and process the roots once they are...

23 February 2021 1,898 1 View

Has anyone done Archard Wear Simulation of GFRP Composite Plate in ANSYS with ACT extension or UDF?

I'm looking to do a sliding wear (plate-on-plate) simulation of GFRP composite plates with Archard Wear Model. Any hints or example steps are appreciated.

17 February 2021 1,447 2 View

Which root in this tap root system, in the picture attached, should be used for root sectioning in order to study the root anatomical details?

There are numerous roots in this tap root system. Kindly suggest or share a research paper where I can clarify the doubts as to which root should be chosen for sectioning and for further root...

14 February 2021 1,816 3 View

Possible problem for showing 0.2 sun intensity instead of 1 sun intensity in AAA class Newport solar simulator?

We have a AAA class Newport solar simulator. We changed the Xenon Arc Lamp recently (XBO450W, Make:OSRAM) as the lifetime got over. However, the intensity is coming to be only 0.2 sun instead of 1...

14 February 2021 9,998 3 View

How can I get access of UNAfold tool?

I am searching for tools to construct molecular beacons which shall be complementary to a given sequence. I don't want to design any primers. I found that UNAfold is one such tool which I could...

02 February 2021 9,065 5 View

The peptide synthesized with CTC resin have mass more (+68 Da) than the desired mass of the synthesized peptide. What could be the reason?

I am synthesizing 7 amino acid long peptide sequence with CTC resin, 50oC coupling for 10 min. On cleavage (TFA/TIPS/Water 95:2.5:2.5) I got peptide with good yield. However, It has 68 Da more...

30 January 2021 8,483 3 View

How do we calculate curvature value in ArcGIS?

Hello everyone, I am trying to prepare curvature map in ArcGIS 10.4, using spatial analyst tool. I am using 10 m CartoDem (projected in UTM 44N). I am getting very different value, curvature...

12 January 2021 504 4 View

How can a publish my case report?

I want to publish a case report regarding jejunal diverticula

02 January 2021 7,630 5 View

How can we maintain the two different DC high voltages of same polarity between parallel electrodes inside the vacuum separated by few millimeter?

I am trying to maintain two different high DC voltages of same polarity (either positive or negative) between two parallel electrodes separated by 500 um inside the vacuum. However, what I found...

21 December 2020 1,735 3 View

What is the most Operating System (OS) which can be INSTALL on Tiny hard devices like Raspberry Pi (RPi) hardware ?

I'm targeting to deploy a mesh network and manually configure MANET routing protocols. I'm preparing scenarios, architectures, and hard devices needed to do that. Are there some step-by-step...

03 March 2021 1,931 5 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

Is there a powerful system for the security of the systems distributed on IoT systems?

02 March 2021 3,858 10 View

How to choose ANN number of hidden layers and nodes?

Hello, Could you please share any interesting research explaining how to choose the number of hidden layers and nodes per layer in case of regression problems using ANN? Thank you, any help would...

01 March 2021 6,200 3 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

What is the exact mechanism of the antimicrobial effect of local anesthetics?

The antimicrobial effect of local anesthetics has been known for more than 50 years, but it still seems to have an unclear mechanism of action. which bacteria? which concentration? etc etc. ....

27 February 2021 4,450 2 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 sample data to increase presence of solar panels in the images?

I am working on creating deep neural network on geospatial dataset and wanted to know how to do the sampling so that I can increase the presence of solar panels in the images. I cannot use entire...

25 February 2021 3,936 6 View

Satellite orbit estimation using Recurrent Neural Network - what should I use?

Hello, I am a master's student studying in Yonsei Univeristy, Korea. I am trying to estimate the state of satellite, using Neural Network. Below is a simple flow of my study. 1. Train (t0 ~ t1)...

23 February 2021 6,383 3 View

Vivi Richard

Hi, I'm also facing the same issue. Simulation running on one node only. If you have discovered solution, can you suggest me ?

Thanks in advance.

Vishnu Chari

Hello Shradheya Raj Rajeshwar Gupta and Vivi Richard , I am also facing the same problem. The only solution I found so far is to use a job scheduler like SLURM, But, currently I am facing problem in correctly installing it. Have you find any solution overcome this without use of a Job scheduler?

Please suggest.

Thanks