Re: Pulling atoms in different directions

From: Chris Harrison (
Date: Sun Mar 29 2009 - 19:05:33 CDT


If you want to use SMD to measure the force for pulling then you can only deal with one vector at a time, as dealing with multiple vectors convolutes (one might even argue "pollutes") the measured force, effectively hiding the true force for a given single vector. At present, for this and other reasons, the code doesn't support multiple SMD vectors.

If you want to pull the layers apart in a single simulation you could investigate the possibility of using tclforces.

If an equilibrium free energy measurement for the "pulling"; as opposed to a direct force measurement; would suffice you could potentially use Adaptive Biasing Force as described in the NAMD manual and ABF tutorial on our website.

One does have to ask though, is there an effective difference between pulling both layers and simply pulling one layer to increase the distance between layers? If there is some sort of effect; dynamical or otherwise; generated at the surface by the pulling force that is otherwise absent in a static layer then I could understand why pulling both layers is necessary.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 217-244-1733              Fax:   217-244-6078
Rahul Bhowmik <> writes:
> Date: Sun, 29 Mar 2009 13:59:01 -0700
> From: Rahul Bhowmik <>
> To:,
> Subject: namd-l: Pulling atoms in different directions
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> Hi All;
> I have two Self Assembled Monolayer (SAM) surfaces facing each other with
> water molecules in between them. Is it possible to pull the two surfaces in
> different direction (say, the top surface is pulled in +x direction and the
> bottom surface along -x direction). I can pulled the one layer (say top SAM
> surface along +x direction) with the following parameters for SMD in
> configuration file:
> SMD  on
> SMDk 5
> SMDFile smd_vel.pdb
> SMDVel 1
> SMDDir 1  0  0
> SMDOutputFreq 100
> Here; the atoms which is being pulled is represented as 1 in O column of
> smd_vel.pdb file.
> How to pull the bottom layer with the same velocity but opposite in
> direction (SMDDir -1  0  0).
> Any help regarding this will be highly appreciated.
> Thank you
> Rahul Bhowmik
> -- 
> ------------------------------------------------------
> Research Associate
> Department of Chemical Engineering
> University of Washington
> Phone: (206) 616-6510
> Email:
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