GROMACS version:2020.4 i installed gromacs and need to know the exchange probability but didn’t got any file holding this name and got only md.log which also didn’t contain exchange probability this the command i run for 36 temperatures for i in 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 do gmx grompp -f nvt_$i.mdp -c em.…

GROMACS version: 2021 GROMACS modification: No Good day, I am trying to perform simulated annealing of a protein (heating from 300K to 350K). I performed generic energy minimization and NVT steps, after that I performed NPT with simulated annealing (300 340). For the production run, I used NPT ensemble. I want to make RMSD plot showing the graphs at 300K and 350K. Should I ma…

Hi all. I have just finished my first MD. Then I did rmsf analysis as follows $ gmx rmsf -s md_0_10.tpr -f md_fit_0_10.xtc -o rmsf.xvg -oq rmsf.pdb -res -b 5000 Then I typed ‘1 (Protein)’ The graph of ‘rmsf.xvg’ is as follows. 스크린샷, 2021-07-13 22-43-311920×1080 143 KB My protein complex has 4 chains and it shows each chain starts from its 1st residue. But, I hope to ge…

GROMACS version: 2020.4 GROMACS modification: No Dear All, I was wondering if anyone had a similar experience and could offer some advice. I’m working with a membrane protein i.e. Nav1.5. Initially roughly about 1.5 years ago, the rat structure for Nav1.5 came out and I simulated this channel and a few mutants in NAMD. I used the CHARMM27 force field and prepared the channel in …