On 7/31/13 6:52 AM, Steven Neumann wrote:
But even though on the other hand that could be more realistic free energy
which could be compare to experiment which also involves ions. Would Justin
please comment on this?
I can offer you nothing more than a hand-waving explanation of what I think
might happen here, so take that for what it's worth. Since you explicitly asked
for my thoughts, such as they are...
The dissociation of the ions may be nothing more than an artifact of the pulling
conditions. Have you tried different force constants and pull rates to see if
this behavior is affected?
On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann <s.neuman...@gmail.com>wrote:
They do not dissociate...Are you sure? My mdp specifies only ligand as a
pull_group1. I think it would change having ions in this group included.
Even though you're not explicitly pulling the ions, they are being forced to
move due to the biasing potential that you are applying.
I would think that sufficient sampling in each window (i.e. enough time that you
might see dissociation of the ions) would provide you with enough information,
but that's hard to predict. My assumption would be that the ions will
absolutely impact the free energy of binding, but from what you said above,
maybe that's right. Maybe it's not. Only way to find out would be to either
exclude the ions or otherwise restrain their initial positions so that you get a
"clean" reaction coordinate involving only the ligand. Then you can decompose
the different contributions to the free energy of binding.
-Justin
On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs <lloyd.ri...@gmx.ch> wrote:
will get the PMF profile for my
ligand binding or ligand and two ions binding?
It would be the ligand and two ions unless the ions also at some point
discossiate from the ligand once in solvent. Could add positional restraint
for them, but dont know how that effects the calculation?
*Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr
*Von:* "Steven Neumann" <s.neuman...@gmail.com>
*An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org>
*Betreff:* [gmx-users] Umbrella Sampling
Dear Gmx Users,
I run SMD to extract the windows for US calculations. The system involves
negatively charged ligand and protein. I generated the protein-ligand
complex within self assembly MD simulations.
I pulled my molecule away and two ions were also detached from the protein
surface being attached to my ligand.
My question: if I run my US caluclation and combine windows by WHAM (I
specified in my umbrella.mdp my ligand as a pull_group1 and same protein
residues I pulled it from as pull_group0) will get the PMF profile for my
ligand binding or ligand and two ions binding?
Steven
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==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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