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Solvate and Grompp Commands - English

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Outline:

About solvent molecule files that can be added to the system Solvate command View the solvated system in VMD About mdp file About grompp command Generate tpr binary file Use dump command to read binary file Find out charge (qtot) on molecule from topology file Add ions with genion command Syntax for adding positive and negative ions

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Pre-requisite

Creating Input Files

Assignment

Code files

input-solvate/
input-solvate/ions.mdp
input-solvate/box-added.gro
input-solvate/topol.top
input-solvate/posre.itp
input-solvate/first.gro

Script

Slides

solvate-and-grompp.pdf
solvate-and-grompp.tex
st-logo-new.png

Additional reading material

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