Farideh Badalkhani

10 Questions 12 Answers 0 Followers

Questions related from Farideh Badalkhani

How can I determine the protonation state of a phosphorene sheet in acidic and neutral pH conditions?

Dear experts, I am going to perform an MD simulation on a system including water and phosphorene sheet in different pH conditions (low and neutral pH). However, I do not know if the different pHs...

12 December 2018 2,524 0 View

How to create a topology file for a receptor-ligand system?

Dear experst, I have got the .itp and .gro files for a drug and a nanosheet from a paper. Then I made the posre file for them using the genrestr command and performed MD simulations on them...

10 October 2018 8,434 6 View

WARNING: Listed nonbonded interaction between particles X and Y at distance ... can anyone please help me with this problem?

Dear all, I am trying to perform free energy calculations of a small drug in octanol using the GROMACS 5.1.3 software. I built a box of octanol using the following command gmx insert-molecules -ci...

03 March 2018 289 0 View

How to find the proper parameters for MM-PBSA calculations using g_mmpbsa package?

Dear experts, I need to perform MM-PBSA calculations using g_mmpbsa package. My problem is that how to determine proper parameters for .mdp file. for example Solute dielectric constant (pdie) or...

06 June 2017 6,749 3 View

What is the best approach to determine box size in an umbrella sampling simulation using Gromacs software?

Dear all, I want to perform PMF calculations on a protein-ligand complex and I am following the Gromacs tutorial. I am using Gromacs 4.6.5. But, I do not know how to find the best box size so that...

11 November 2016 3,661 5 View

How to determine the time needed for each window in umbrella sampling?

Dear all, Is there any criteria to determine the optimum run time for each window in umbrella sampling? My receptor has equilibrated after 30 ns of MD. Should I consider the same run time for each...

11 November 2016 652 4 View

How to calculate radius of gyration?

Dear all, Could somebody help me on a proper script to calculate radius of gyration in molecular dynamics simulations? I am using the NAMD software and VMD as visualization software. Regards, Farideh

05 May 2016 2,238 2 View

What is the reason of blowing up a system in a simulation?

Dear all, I am performing a MD simulation on a branched polymer through GROMOS 53A6 force field. But, I don't know why when I execute the energy minimization, the system blows up. I have attached...

09 September 2015 9,661 4 View

What is the best Force Field for MD simulations on Drug-Dendrimer systems?

Dear all, I'm looking for a proper Force Field for MD simulations on Drug-Dendrimer systems. Could you suggest a good FF for this reason? It is mentionable that Im working with GROMACS software.

02 February 2015 9,160 3 View

How can I understand the umber of ligands can dock into a receptor?

Hi,I want to dock a ligand into a receptor with AutoDock Vina software, Is there any way to understand how many ligands can dock into a receptor, ifwe do not have any experiment date?Best...

01 January 2015 9,665 7 View