How to calculate radius of gyration?

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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...

11 December 2018 2,537 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...

09 October 2018 8,448 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...

02 March 2018 317 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...

05 June 2017 6,768 3 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...

10 November 2016 665 4 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...

10 November 2016 3,674 5 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...

08 September 2015 9,674 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.

01 February 2015 9,173 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...

31 December 2014 9,677 7 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Some new emerging problems on application of RL for scheduling in IoT networks?

I have seen plenty of existing works on applied Reinforcement Learning (RL) policies for optimized scheduling in IoT networks including Q-learning, DQNs, and the newer ones including PPO for...

01 August 2024 8,754 2 View

Transfection in HEK293T cells?

Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...

31 July 2024 9,892 4 View

How to retain the a GFP tagged gene expression in stable cell line?

Hello , I established a stable cell line expressing GFP tagged to a centrosomal gene having G418 drug selection marker. I validated the stable line by IFA and Western blotting, results are fine....

29 July 2024 5,007 0 View

Hi there, someone has the SeinFit software for windows because I cannot download it?

DOS version.

29 July 2024 6,064 1 View

There is possible way to calculate experimental DOS from the UPS spectrum of the material. How to calculate the DOS from UPS?

Here, I have attached the UPS graph. I'm trying to calculate the DOS/DOVS from the UPS.

29 July 2024 4,971 1 View

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 View