Re: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs

From: dbaogen (
Date: Thu Dec 12 2013 - 23:58:49 CST


      Thank you firstly. I checked the Gromacs manual. And I found that the "distance" option which pull along the vector connecting the reference and pull groups was used.
Would you please be kind to explain the algorithm of "distance steering" briefly or recommend some references. Thanks again.

Duan Baogen

From: Aron Broom
Date: 2013-12-13 09:25
To: dbaogen
CC: Norman Geist; namd-l
Subject: Re: AW: namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
I may be missing something crucial in terms of what SMD does, but wouldn't running it without that harmonic restraint be meaningless? What I mean is, don't you want to steer the ligand relative to the protein? So either you should perform this steering on the distance between the protein and ligand, or, you just do the ligand but hold the protein fixed (with say a harmonic restraint on the Ca as you say).

I've never done SMD, and don't know much about how it is supposed to work, but if all you do is yank on the ligand, the only information I can see you getting from that is maybe something relating to the energy barrier for ligand dissociation, and by that I mean the kinetic one, not the thermodynamic one.

Are you sure in the Gromacs case it wasn't the distance between the ligand and protein that was being steered? Or maybe the restraint is implicitly assumed and that's why they don't mention it?

On Thu, Dec 12, 2013 at 8:02 PM, dbaogen <> wrote:

     Thanks for your suggestion. Using SMD in NAMD software, if we impose harmonic restriction on the center of alpha carbons of protein, the ligand can be pulled out. But I am not sure whether this will introduce artificial effect on the simulated system. Would you like to give me some suggestions about the simulation. Thanks.

Duan Baogen

From: Norman Geist
Date: 2013-12-10 22:18
To: 'dbaogen'
CC: Namd Mailing List
Subject: AW: namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
I doní»t think that this is a problem of the implementatio of the pulling. Ití»s more likely a stronger interaction between your protein and the ligand than in the publication you found. Maybe you could give the proteins center of mass a counter force.
Norman Geist.

Von: [] Im Auftrag von dbaogen
Gesendet: Dienstag, 10. Dezember 2013 13:02
An: namd-l
Betreff: namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs

Dear all,

            Recently, I have a problem in using SMD to pull a ligand out from the protein active site. In the course of pulling, the protein is moving along with ligand. So the results are not consistent with our expectation. If we impose the harmonic restraint on protein, the ligand can be pulled out. But the artificial effect would be introduced if we did it like that. Would anyone like to give me some suggestions about the SMD simulation in NAMD?

          In addition, it is found that the pull code in Gromacs can also do the SMD simulation. From the published results using pull code in Gromacs, the protein itself was not restricted while pulling a ligand out from the protien's active site. Would you like to explain the difference between SMD in NAMD and pull code in Gromacs? Thanks in advance!


Duan Baogen

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Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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