How to use reduced unit in gromacs?

Dear researchers, I am using gromacs for molecular dynamics simulation. These days, I am working on lennard jones fluid. In lammps, it is easy to use reduced unit by just set the parameter as 1....

01 February 2019 7,304 2 View

Can I make shell script for gmx rdf?

I want to make shell script for calculating rdf. I want to make a lot of rdf.xvg files for each time step. Here's my approach. #!/bin/bash for i in $(seq 1.1 .01 30.0) do echo -e "OH2\nOH2\n"...

11 December 2018 8,965 0 View

How to generate supercritical CO2 in gromacs?

Is there any procedure that I can adapt? or If there's some paper, please let me know. With my respect

10 November 2018 8,116 0 View

How to calculate tetrahedral order parameter in gromacs?

I have 50 ns simulated bulk water system. For analysis, I want to calculate tetrahedral order parameter q. I am using gromacs, and I know the command "gmx hydorder". However, I don't know how to...

09 October 2018 6,779 3 View

Tetrahedral order parameters and local water configurations?

I have configuration simulated with gromacs, NPT for 50 ns. During analysis, I got problems. 1. tetrahedral order parameter q 2. Double donor and single donor configuration division(reference of...

09 October 2018 8,496 0 View

How could I calculate voronoi volue of water?

I am trying to calculate voronoi volume of a water surronded by nearest oxygen. This is my code. from numpy import * import glob box = 3.73014 list_of_files =...

09 October 2018 523 4 View

Does anyone knows how to install drude implementation files for gromacs?

I installed drude implementation files from charmm website. Here's URL: http://mackerell.umaryland.edu/charmm_drude_ff.shtml. On my linux server Downloads directory, I did the procedure 1. git...

08 September 2018 9,901 2 View

Does anyone know how to simulate swm4-ndp in gromacs?

I am recently using gromacs to simulate bulk water. I modified existing swm4-ndp.itp file and did the 10bs NPT after 200ps NVT. But the problem is result. Energy, density and volume is nice, but...

08 September 2018 5,039 0 View

Could anyone help me inderstanding Soft matter lattice model?

In the lattice model in soft matter physics, average number of solute and solvent pair is calculated by = zNtotV(1-V) where z is coordination number and V is volume fraction for the solute...

02 March 2018 722 0 View

How can i insert molecules inside in gromacs?

I want to insert molecules inside the wall. Configuration is like below. I want to put some ions inside the wall surrounding polymer. Please help me. YK Lee

01 February 2018 9,661 2 View

Do you know any MR image dataset?

I would like to research on MR images (0.5T and 3T). Can you please suggest some websites that I can download dataset including both 0.5T and 3T MR images? Thank you.

02 March 2021 7,735 3 View

Do you know good and user-friendly programs to measure plant quantitative traits?

For my research i will need to measure plant quantitative traits (especially leaves area and roots length, but would be nice to add some more information). I recently discovered...

01 March 2021 5,035 2 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View

Any suggestions for a website that allows you to create questionnaires and gather unlimited data (Totally free)?

I have found only four of them; www.surveyplanet.com www.online-anket.gen.tr www.surveey.com and of course google forms. Expecting to see your suggestions if there is any. Thank you

28 February 2021 3,237 3 View

What is Flat Lens Antenna?

28 February 2021 5,433 3 View

Do I need to ask permission to use pictures for my questionnaire?

I would like to use some photo from a government website for my questionnaire. But, different photo is from the different owner. So, should I just get permission from that government body or still...

23 February 2021 1,631 3 View

Why does the sum of reaction forces not match the force component of a Free Body Cut in Abaqus?

I am using Abaqus to simulate a plate with in-plane loading. The boundary conditions allow the right edge to move up and down, the displacements on the left edge are fixed. There is no rotation...

23 February 2021 711 3 View

How can I get the coding gene sequences of Hela and U2OS cell lines? Is mRNA sequence of Hsp90 alpha tissue specific??

I am looking for hsp90 mRNA sequence in Hela and U2OS cell lines, I have tried through ncbi but always the output is hsp90 in homo sapiens not in the specific cell line. Kindly, could any one...

22 February 2021 1,853 3 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

How do you interpret multiple meta-regression in STATA?

Please could someone recommend a resource that explains performing meta-regression with multiple moderators. I have read the STATA META ANALYSIS REFERENCE MANUAL, but this only gives examples of...

17 February 2021 7,376 1 View