Gaussian cub output is not overlapping with isosurface ?

I want to do Bader charge analysis and I have observed that the cub file generated from gaussian have problem in overlapping to its surface when opened in Vesta. any suggestion what could be done...

07 August 2018 2,181 4 View

How to design hairpin model structure for DNA

I want to simulate hairpin DNA with drug complex, but I found it difficult to design pdb file for hairpin DNA. I tried few available online resources but can not design, the sequence I am using is...

07 August 2017 2,324 7 View

Interaction energy from md trajectories.

I used namdenergy plugin in vmd to extract total, vdw and electrostatic energy. I am confused to know about the energy provided by apbs/mmpbsa. How it is different from the data obtained from...

09 October 2016 3,405 3 View

How to make double stranded cDNA from single stranded cDNA?

03 April 2016 5,477 8 View

What kind of raman shift could be observed from peptide?

I had a peptide, I am trying to get raman spectra of peptide, I found in literature, the shift in peak could be observed. What kind of shift could be observed red/blue and Why? I had done some...

09 October 2015 4,447 5 View

How do I calculate the number of close contact and contact area between receptor and ligand?

02 March 2015 2,836 7 View

Can we do umbrella sampling and SMD by CHARMM or NAMD?

I want to do Umbrella Sampling (US) using NAMD, my confusion is as follows: 1. US can be perform using SMD, therefore, how to decide the SMD config file input is correct or not? What input CV or...

10 November 2014 5,450 3 View

Can anyone help me to design a new force field for a small organic/inorganic molecule for NAMD?

06 July 2014 8,981 16 View

If we want to know the result output from a NAMD simulation, what different results could be obtained?

I am new to NAMD and recently run a simulation of DNA-organic molecule interactions in NAMD for 20 ns. I want to know what the different results are that I should analyze using the output of the...

05 June 2014 1,975 6 View

How are the parameter files for new force field constructed?

I need to know the procedure and required tools for the construction .par, .inp, .tcl files

10 November 2013 6,960 2 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

What are the new 2D nanomaterials were used for Silver nanoparticles stabilization?

In the stabilization of AgNPs are vital in current research interest. However, some of the 2D nano-materials like graphene oxide, MoS2, etc... previously used to stabilize it. But still they shown...

01 March 2021 2,207 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

Can impedance of antenna be less than 50 ohms?

I am simulating helix antenna in hfss, right now, giving excitation with 50 ohms port. When I see the results of Z parameter (real). It shows lower than 50 ohms. Do not understand, if it can be...

27 February 2021 4,218 7 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

Thermal reduction of graphene oxide.?

I am trying to reduce graphene oxide by thermally but I have no proper information regarding this. Can any one help me regarding the details about temperature and time for the reduction of...

23 February 2021 4,155 4 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 find out the problem of VMD software when i run it?

Hello I try to install and run the VMD software on windows 10 (64-bit).It doesn`t work and it is closed when I run it. I checked all of tutorials, videos and documents. But they did not work...

22 February 2021 8,211 3 View

Is there an ideal incubation time of RGO-modified SPCE before subsequent use, i.e., electrochemical characterization or further modification?

I notice that upon washing and air-drying of my RGO/SPCE surface and characterizing again via DPV, the current response towards ferricyanide probe significantly decreases. My worry is that the...

22 February 2021 5,324 3 View