Re: Steered MD diminishing distances

From: Giacomo Fiorin (
Date: Sat Apr 02 2016 - 20:56:34 CDT

Hi Giulia, you could suitably reverse the sign of SMDDir, or use a moving
harmonic restraint on the interatomic distance, defined using the
collective variables module. The colvars chapter of the manual has an
example input with the harmonic restraint, and you should just add the
necessary keywords to make the harmonic restraint a moving one.


On Sat, Apr 2, 2016 at 9:29 PM, giulia palermo <>

> Dear all,
> I am usindg Steered MD simulations in otder to approach two groups in my
> system.
> Usually, by employing Steered MD, one wants to move far away two atoms
> or groups.
> I would like to do the conrary: approach two selected groups. My
> configuration file is the following.
> I want to steer my atoms along the SMDDir vector, but I am not able to
> approach the teo atoms, since the code pulls them far apart.
> Could you please help me in that?
> Thank you very much
> Best wishes
> Giulia Palermo
> #Steered MD
> SMD on
> SMDFile reference_smd.ref
> SMDk 20
> SMDVel 0.00001 # 0.00001 A/timestep = 5 A/ns (2 fs timestep)
> SMDDir 0.377 0.911 0.169
> SMDOutputFreq 5000

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 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
Lab page:
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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