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

Polarizable water model ?

Does anyone know where could I find polarizable water model force field and coordinate file? I looked it up in martini website, but there's no one-bead polarizable model. Rather, they suggest 3...

06 July 2018 5,054 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

Polymer composites suddenly solidifies?

I am making polymer composite by solvent mixing method. When I am trying to add filler solution in polymer solution it quickly get solidified. How to make them then uinform? It doesn't give time...

03 March 2021 7,540 4 View

What solvent can I used for Paal Knorr reaction between 6-amino hexanoic acid and 2.5 hexanedione?

I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...

02 March 2021 4,443 2 View

How to polymerize TEOS?

I want to polymerize TEOS on a surface. I know that NH4OH is a preferred catalyst and an alcoholic solvent should be used .But I can not find certain amounts of each material to use. Does any one...

02 March 2021 1,404 6 View

What does Servant Leadership mean today and in the future? What are the advantages and disadvantages?

In current time of many changes in business and world of work, a lot is said and reported about the importance, skills and benefits of leadership. Are soft skills becoming more and more important?...

02 March 2021 8,149 3 View

How can extract ciprofloxacin hydrochloride disolve in water er to organic solvent such as dichloromethan or any other solvent?

I need a procedure to extract the ciprofloxacin hydrochloride from aqueous solution by using dichloromethane in detail,. I thank you very much.

01 March 2021 4,306 1 View

How to separate water from glycerol solvent in a solvent recovery vacuum distillation column?

I am currently doing my third year design project. I have been assigned to design a glycerol recovery column in vinyl acetate monomer production. The process unit before the recovery column is an...

01 March 2021 9,525 4 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

How to make fractions of chloroform extract of plant, using seperating funnel?

28 February 2021 8,466 2 View

Why am i not getting solid after reacting APTES with salicylaldehyde?

The reaction of APTES with salicylaldehyde in ethanol leads to the formation of imine compound yellow solid which is mention in literature, but I am not getting yellow solid I don't know why? when...

28 February 2021 2,955 2 View

can I treat waste water containing solvents and alcohol with electrocoagulation?

there are solvents and alcohol in the waste water of a factory that produces disinfectants. Increasing this waste water requires very serious operations. Can I treat this waste water with...

27 February 2021 2,609 3 View