Re: SMD negative forces

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Apr 03 2019 - 10:18:06 CDT

 

Hi Steve,

 

Another way to solve the issue is to use the pdb from the last step of the previous simulation to set the SMD atoms (SMDFile).

 

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: "Seibold, Steve Allan" <stevesei_at_ku.edu>
Date: Wednesday, April 3, 2019 at 10:14 AM
To: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Subject: RE: namd-l: SMD negative forces

 

Thanks Joao for pointing that out. I failed to make the connection when I read the tutorial..That explains it….

 

 

From: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Sent: Wednesday, April 3, 2019 10:00 AM
To: namd-l_at_ks.uiuc.edu; Seibold, Steve Allan <stevesei_at_ku.edu>
Subject: Re: namd-l: SMD negative forces

 

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

 


image001.png image002.png image003.png

This archive was generated by hypermail 2.1.6 : Mon Sep 16 2019 - 23:20:31 CDT