Why extended simulation dose not start at 0 point?

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MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

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MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

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fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

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fatal error

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fatal error

16 June 2021 0 0 View

fatal error

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How to analyze a particular region of my simulation box in GROMACS?

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Why are the velocities so high in my Boussinesq approximation Fluent simulation?

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Tasneem Kausar

Merge trajectory files (600+9400) then calculate RMSD.

Mokhtar Nosrati

Hi, you should merge two file for fix your problem

Christian Jorgensen

You need to use trjcat

gmx trjcat -f *.xtc -o out.xtc

Then use gmx check to get the exact number of frames

gmx check -f out.xtc

Alireza Mohebbi

I have tried the code but there is something strange here in my files. I do not have .xtc related to extended simulation. Only a .tpr file is for extended simulation.