Whta is the output force filed in the topology from Acpype?

Dear all, I generated topology of a ligand (ATP) using Acpype which gave me the topology file topol.top and conf3_GMX.itp. I'm writing a report and confused as to what I should write in the...

03 April 2019 3,579 3 View

OPLS force field with Acpype GeneratedTopology?

Dear all, Can we use the .itp file generated by Acpype with OPLS forcefield, is it compatible? I know Acpype uses antechamber which is based on GAFF but the question is whether the .itp file can...

01 February 2019 7,030 1 View

How to change color of particular atom in VMD?

Dear all, I want to change only the color of an atom with index 10 in vmd and keeping rest of the atoms in default. Is there a way to do this in vmd? Thanks and Regards, Raghav

31 December 2018 3,202 2 View

How to use gromacs pdb2gmx for ATP molecule?

Dear all, In gromacs tutorial its written that pdb2gmx can be used for cofactors like NAD(H) and ATP, my question is how can i use it on my pdb file of ATP molecule. Do i need to change the...

31 December 2018 275 5 View

How to get an OPLS-AA topology for ATP(Mg2+) complex?

Dear all, I want to generate the topology for ATP(Mg2+) complex using OPLS-AA force field. For only ATP i used Acpype and it worked but when I used ATP(Mg2+) acpype is not working, that's...

31 December 2018 2,032 5 View

How to change Bond Radius of Dynamic Bond Representation in VMD?

Dear all, In VMD Dynamic Bond Representation the Bond Radius can't be set below 0.1. Is there a way to do it using TK console? I want to reduce the bond radius further to like...

31 December 2018 428 1 View

Where to get the structure of ATPMg+2 complex?

Dear all, Where can I get the structure of ATPMg+2 complex for my simulations? I need a starting structure for my MD simulations. Thanks and Regards, Raghav

31 December 2018 2,353 3 View

How to calculate charges from cp2k output MD-pos-1.xyz file?

Dear all, I have this cp2k output file from a MD run MD-pos-1.xyz which has iteration number vs atomic coordinates information. I want to calculate charges for each atom for each...

10 November 2018 9,404 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 to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

How can the modification of garden soil cause global warming?

Hello, I am working on a soil project and I found a primary research article that tests how the modification of agricultural soil can cause global warming, using a thermal collector, however I...

02 March 2021 7,161 3 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

Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...

01 March 2021 3,610 1 View

Does anyone know to clarify these changes?

01 March 2021 1,290 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 convert .vesta file to a .cif file?

I've used the "export data" option in Vesta software to convert my unit cell into a cif file however when I use that cif in atomsk it shows error such as "can't read the position of atom 0". If I...

28 February 2021 4,966 3 View

What is Flat Lens Antenna?

28 February 2021 5,433 3 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