Gabriela de Lima Menezes

5 Questions 10 Answers 0 Followers

Questions related from Gabriela de Lima Menezes

Which temperature should I use in Molecular dynamics (GROMACS) for a protein found in endoplasmatic reticulum?

Hi everyone, I'm trying to perform a MD simulation for a protein found in ER. In mdp file should I set: ref-temp= 300 K or 310K? gen-temp should be the same than ref-temp or 300...

06 June 2019 6,453 7 View

How to compare two RMSD plot (frame vs frame) from gromacs?

I have two proteins. One is wild-type and the other is a mutant. The RMSD plot (nm vs time) showed me mutant is far more unstable. But, when a plot the RMSD frame vs frame graphic it seems mutant...

05 May 2019 4,699 8 View

How to study protein dimer formation by using molecular dynamics simulation (GROMACS)?

I have a dimer protein. I want to study monomeric conformation changes and see, by using molecular dynamics, how dimer is created. Maybe study transitional conformations. I don't know. Does anyone...

01 January 2019 5,534 4 View

Fatal error doing restart in GROMACS 2018?

hello guys! I am using the following command to restart my protein simulation that has stopped in 60 ns (total simulation is100 ns) > gmx mdrun -v -deffnm 6_md -cpi 6_md.cpt...

01 January 2019 1,769 3 View

What this "Fatal error: x particles communicated to PME rank 10 are more than 2/3 times the cut-off (...)" means?

Can anyone help me? I am trying to perform MD simulation. My glicoprotein is a dimer (two different chains). When I run NVT with restriction this fatal error appears: "Fatal error: 12 particles...

11 November 2018 8,734 2 View