Rahmaditya Eka Putri

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Questions related from Rahmaditya Eka Putri

How to make a protein solvated with 5 M NaCl system in PACKMOL?

I used to do this solvation by doing these steps: 1. found the box volume information from gromacs by choosing the distance between the outer side of protein and the box randomly (I set it to 22...

26 August 2020 9,718 0 View

How to calculate rmsf calculation based on C-alpha (or per residue) in gromacs?

I chose C-alpha as a group for root mean square calculation(rmsf), but why my rmsf calculation in gromacs did still count on atom-based, not residue-based? The command I used: gmx rmsf -f...

18 August 2020 1,491 6 View

Why the dat files cannot be opened properly in xmgrace?

Hi, I did not know really much about xmgrace, so there's an unsolved problem I got: I wanted to open and plot the data within a dat file in xmgrace. I clicked Menu Data --> Import --> ASCII -->...

17 August 2020 2,404 2 View

How to simulate a 5M NaCl solvated protein with two Ca2+ ligands in GROMACS properly?

Hi, I'm kinda new to computational biochemistry. so here are some few questions of mine: I made an amylase system solvated with NaCl 5M via PACKMOL, and the pdb file of solvated amylase was...

10 August 2020 2,578 2 View