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 9,758 0 View

How to determine the right box size of protein for solvation with PACKMOL? and how to get to know the salt concentration of a saline system?

The steps I had done: 1. I built box with pretty far distance from the outer surface of protein to the box side (-d = 20.0 A), and I thought this size had been too big for average distance used...

26 August 2020 2,127 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 1,554 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 2,488 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 2,629 2 View