Hello,
I used gromacs 2020 and performed the 100ns simulation protein drug complex. I generated .tpr file for 100ns simulation using gromacs version 5 as g_mmpbsa works with gromacs 5x version only. Now I would like to know command to compute g_mmpbsa every 20ns. I am using .xtc (generated from gromacs 2020) and .tpr file generated from (gromacs 5x).
Thank you,
Sainitin
Hi,
this is the general command:
"g_mmpbsa -s file.tpr -f traj_comp.xtc -mm -pol -apol -mmcon -pcon -apcon -mme -pbsa -decomp -i mmpbsa.mdp -n mmpbsa.ndx -incl_14 -dt 20000".
But I would suggest you to discard the initial portion of the MD run as equilibration and only to use the last 50 ns:
"g_mmpbsa -s file.tpr -f traj_comp.xtc -mm -pol -apol -mmcon -pcon -apcon -mme -pbsa -decomp -i mmpbsa.mdp -n mmpbsa.ndx -incl_14 -dt 1000 -b 50000".
Hi,
If you don't want to have to use the old 5x version of gromacs you could use the gmx_MMPBSA add-on instead:
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/getting-started/
It works with the newest version of gromacs no problem.
Hello Dr Sainitin Donakonda
I already performed simulation for 100ns of my complex using Gromacs2020. It would be great if u can share with me on how to generate .tpr using Gromacs ver5, so i can run mmpbsa using abovementioned commandline.
Thank you in advance
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