Steered MD diminishing distances

From: giulia palermo (
Date: Sat Apr 02 2016 - 20:29:14 CDT

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

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