Re: SMD negative forces

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Apr 03 2019 - 10:00:17 CDT

Hi Steve,

 

The reason that you are seeing the system getting back to the initial position is that the SMD relies on the timestep to evaluate the position of the dummy atom pulling the SMD atoms (“ where is the number of elapsed timesteps in the simulation and is the size of the timestep in femtoseconds.”

 https://www.ks.uiuc.edu/Research/namd/2.13/ug/node46.html and https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node18.html)  

 

To fix this, set the firstTimestep as the last timestep from the previous simulation.

 

I hope this helps

 

Best

 

João

 

 

……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois

http://www.ks.uiuc.edu/~jribeiro/

jribeiro_at_illinois.edu

+1 (217) 3005851

 

From: <owner-namd-l_at_ks.uiuc.edu> on behalf of "Seibold, Steve Allan" <stevesei_at_ku.edu>
Reply-To: <namd-l_at_ks.uiuc.edu>, "Seibold, Steve Allan" <stevesei_at_ku.edu>
Date: Friday, March 29, 2019 at 8:42 AM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Subject: namd-l: SMD negative forces

 

I have a question on Steered MD. I have been doing multiple pulling simulations and noticed that every time I restart the pulling simulation, I get hundreds of beginning steps with a negative force and hence, in the VMD representation, the system “falls” back from its initial position (i.e. relaxes to its start position) before it starts pulling (with positive force) again. Why is this? Is it because the output (used for restarting) contains no force history? Is there a way to stop this? Am I doing something incorrect?

 

Thanks Steve

 


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