Fateme Akhondfeyz

4 Questions 1 Answers 0 Followers

Questions related from Fateme Akhondfeyz

How can I specify the value of colvar parameters in umbrella sampling with NAMD?

I am going to run an umbrella sampling to measure the PMF for passing ion from channel in NAMD software. I wanna know how can i find out the value of these parameters: width, lowerboundary,...

30 May 2024 8,896 0 View

How merge output files of simulation with NAMD?

I have been running steered molecular simulation with NAMD, but in the middle of my simulation it has stopped and i have restarted from specific steps which had stopped. Finally i have two parts...

20 May 2024 1,520 2 View

Have you ever run a steered molecular dynamic simulation with NAMD?

Hi everyone. Is there anybody here who have run a steered molecular dynamic simulation with NAMD and knows about the parameters which i have to write in my configuration file?

06 March 2024 7,976 1 View

How could i minimize and equilibrate system with available output files of CHARMM-GUI for NAMD?

I have downloaded output files of CHARMM-GUI for NAMD which i had made membrane-protein complex with CHARMM-GUI and now i don't know what should i do with these files before running simulation...

14 February 2024 4,217 0 View