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Questions related from Gabriela de Lima Menezes
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 6,452 7 View
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 4,697 8 View
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 5,533 4 View
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 1,768 3 View
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 8,730 2 View