From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Dec 13 2013 - 00:47:03 CST
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, wouldn't
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 <mailto:broomsday_at_gmail.com>
Date: 2013-12-13 09:25
To: dbaogen <mailto:dbaogen_at_gmail.com>
CC: Norman Geist <mailto:norman.geist_at_uni-greifswald.de> ; namd-l
<mailto: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 <mailto:norman.geist_at_uni-greifswald.de>
Date: 2013-12-10 <tel:2013-12-10%C2%A022> 22:18
To: 'dbaogen' <mailto:dbaogen_at_gmail.com>
CC: Namd Mailing List <mailto:namd-l_at_ks.uiuc.edu>
Subject: AW: namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
Hi,
I don't think that this is a problem of the implementatio of the pulling.
It'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: 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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