Re: SMD pulling speed

From: Giacomo Fiorin (
Date: Sat Sep 27 2014 - 21:16:15 CDT

In theory you can run ABF on top of SMD, but only if you disable the
biasing force. Alternatively, get rid of the SMD and just go with ABF.

You cannot use two concurrent free energy calculation / enhanced sampling
methods at the same time if they both apply forces to the system. The
results are meaningless from the thermodynamical point of view.


On Sat, Sep 27, 2014 at 9:45 PM, Charles Whidborne <> wrote:

> Hi,
> I am trying to perform a steered molecular dynamics simulation on a DNA
> molecule to pull a small piece of DNA from a longer strand. I have a
> pulling speed of 5A per nanosecond, pulling mainly in the x direction and a
> harmonic constraint on the longer DNA strand so it doesn't move when pulled
> (to allow strand separation). I also have ABF set on the small strand to
> measure the PMF because i want the free energy of the separation of the
> strands. However, after about 1ns the strand has moved about 20 angstroms
> from the initial position, having moved much faster than I expected, the
> remainder of the simulation i see a more or less constant pulling of 5A/ns.
> Have I done this correctly?
> I have also read that during SMD, it is advisable to turn off the langevin
> thermostat (possibly replacing it with lowe-anderson) due to dragging
> forces on the SMD atom, how do I measure or know that there are dragging
> forces on my atom? and can this alter the free energy i'm measuring so that
> it gives and incorrect value?
> colvars on
> colvarsConfig
> SMD on
> SMDFile 19-6Trip-1net.pdb
> SMDk 2
> SMDVel .000005 ;# 5 A/ns = .005 A/ps = .000005 A/fs
> SMDDir 1.254 0.229 0.00
> SMDOutputFreq 100
> constraints on
> consexp 2
> consref 19-6Trip-1net.pdb
> conskfile 19-6Trip-1net.pdb
> conskcol B
> selectConstraints on
> selectConstrX on
> selectConstrY off
> selectConstrZ off
> Cheers,
> Charlie

Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704C
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213

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