Asma Feriel Khoualdi

3 Questions 4 Answers 0 Followers

Questions related from Asma Feriel Khoualdi

I don't get .vel .coor and .xsc files when I run equilibration steps using CHARMMGUI generated input files?

Hello, I ran the attached script but don't get all the output files needed to proceed to step6.2. Specifically, step6.1_equilibration.coor and step6.1_equilibration.vel and...

09 April 2020 8,003 1 View

How to analayse equilibration status after CHARMM GUI equilibration input files are submitted on slurm server?

Hello, I am new to Molecular Dynamics and eager to know how do I begin analysing. I will divide my query into points as follows: 1)I used namd2 command to get the output into an...

18 March 2020 4,412 3 View

How to add ions in channel pore and solvate the protein to set up pdb for MD simulation?

Hello, I am using CHARMM-HMMM builder to generate my input files, but I want to set up my pdb for HCN1 channel by adding 4 K+ ions in the pore and solvating it, but I don't know how to do that....

12 March 2020 2,681 1 View