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

From: Aron Broom (broomsday_at_gmail.com)
Date: Sun Dec 15 2013 - 00:51:33 CST

Duan,

I think the overall picture here is that before delving into specific
methods, you may want to review articles on MD, and thermodynamics, so that
you have a clearer sense of the general ideas behind all the biasing
methods.

~Aron

On Fri, Dec 13, 2013 at 2:43 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> Of course I meant negated.
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Norman Geist
> *Gesendet:* Freitag, 13. Dezember 2013 07:47
> *An:* 'dbaogen'
> *Cc:* Namd Mailing List
> *Betreff:* AW: Re: AW: namd-l: puzzle of SMD in NAMD-2.9 and pull code in
> Gromacs
>
>
>
> If we believe what Newton told us, any force will have an equal negotiated
> counter force. So anyway, to conserve the energy in your system, wouldnt
> you need a counterforce to the COM of the protein in any case when pulling
> the ligand away?
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *dbaogen
>
> *Gesendet:* Freitag, 13. Dezember 2013 06:59
> *An:* Aron Broom
> *Cc:* namd-l
> *Betreff:* Re: Re: AW: namd-l: puzzle of SMD in NAMD-2.9 and pull code in
> Gromacs
>
>
>
> Hi,
>
>
>
> 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.
>
>
>
> Best
>
> Duan Baogen
>
>
>
>
>
>
>
> *From:* Aron Broom <broomsday_at_gmail.com>
>
> *Date:* 2013-12-13 09:25
>
> *To:* dbaogen <dbaogen_at_gmail.com>
>
> *CC:* Norman Geist <norman.geist_at_uni-greifswald.de>; namd-l<namd-l_at_ks.uiuc.edu>
>
> *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 <dbaogen_at_gmail.com> wrote:
>
> Hi,
>
> 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.
>
>
>
> Best
>
> Duan Baogen
>
>
>
>
>
> *From:* Norman Geist <norman.geist_at_uni-greifswald.de>
>
> *Date:* 2013-12-10 22:18
>
> *To:* 'dbaogen' <dbaogen_at_gmail.com>
>
> *CC:* Namd Mailing List <namd-l_at_ks.uiuc.edu>
>
> *Subject:* AW: namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
>
> Hi,
>
> I dont think that this is a problem of the implementatio of the pulling.
> Its 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:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *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!
>
>
>
> Best
>
>
>
> Duan Baogen
>
>
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> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
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-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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