Nadim Ferdous

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Questions related from Nadim Ferdous

How to model a query protein having 3036 residues?

I need to model a protein having 3036 residues and it doesn't have any good template. I tried I-Tasser, Robetta, tr-ROSETTA and they have a limit of 1200 residues. I also tried AlphaFold colab...

16 June 2022 6,659 1 View

How to get the final structure of a protein-ligand after performing 100ns MD simulation using GROMACS?

I have performed a 100ns simulation of a protein-ligand complex. Now I want to get the final structure of the complex after simulation and superimpose it with the initial structure. What is the...

01 April 2021 8,526 4 View

How to decrease use of CPU cores and GPU percentage in GROMACS?

During any simulation of complexes using GROMACS utilizing all the 12 cores and around 90% of GPU, my pc GPU temperature reaches up to 85 degree celcius. Is there any way to decrease the...

27 March 2021 8,747 2 View

How to restart simulation in Gromacs?

I tried to run a 500ns MD simulation of a protein in Gromacs. Due to power failure, my pc turned of after around 450+ ns. Now I want to restart the simulation from that point. I used the following...

14 November 2020 9,355 3 View

How to calculate RMSF per residue name vs time in Gromacs?

I have done 100ns simulation using Gromacs. To calculate the RMSF, I used the following command- gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res But when I plotted the graph in excel, I found...

13 November 2020 4,856 2 View