Re: [gmx-users] how to use gromacs for steered molecular dynamics(SMD)

Nilov Dmitri nilovdm at
Thu Oct 9 13:54:26 CEST 2008

See AFM pulling description in manual. 
AFM means "Atomic force microscopy".
That`s what you neeed).

-----Original Message-----
From: "huifang liu" <huifangliu1985 at>
To: gmx-users at
Date: Thu, 9 Oct 2008 14:09:05 +0800
Subject: [gmx-users] how to use gromacs for steered molecular dynamics(SMD)

> Hi, gmx-users
> i want to use gromacs to pull a small ligand through a protein channel and
> study the interaction between the ligand and the protein during this
> process. However, i have not found out any useful information about steered
> molecular dynamics(SMD) using Gromacs software.
> What are the differences between SMD and general MD in using Gromacs and how
> to set up the related parameters?
> Thanks a lot.
> Dove.
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Nilov Dmitri

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