Dear Justin and Gmx Users,
I run a pulling of my ligand away from my protein with the same mdp file
and I obtained two different plots - Force vs time (The breaking point
occured at different times with different force). Can you please explain?
My mdp file:
title = Umbrella pulling
Steven Neumann wrote:
Dear Justin and Gmx Users,
I run a pulling of my ligand away from my protein with the same mdp file
and I obtained two different plots - Force vs time (The breaking point
occured at different times with different force). Can you please explain?
If you change the
On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Justin and Gmx Users,
I run a pulling of my ligand away from my protein with the same mdp file
and I obtained two different plots - Force vs time (The breaking point
occured at different
Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Justin and Gmx Users,
I run a pulling of my ligand away from my protein with the same
mdp file and I obtained
On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Justin and Gmx Users,
I run a pulling of my
Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu
On Mon, Feb 20, 2012 at 8:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul
Steven Neumann wrote:
On Mon, Feb 20, 2012 at 8:07 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu
Would you recommend position restrained of the protein backbone atoms or
e.g. residues from the lower part so that the protien will not roatate?
On Fri, Feb 17, 2012 at 10:41 AM, Steven Neumann s.neuman...@gmail.comwrote:
Hello Justin,
As you recommended I run longer pulling of my ligand. I
Steven Neumann wrote:
Hello Justin,
As you recommended I run longer pulling of my ligand. I pull the ligand
which is on the top of my protein so the top of the protein is pulled so
that the whole protein rotated app. 30 degrees - the low part of the
protein came out of the box due to the
On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Hello Justin,
As you recommended I run longer pulling of my ligand. I pull the ligand
which is on the top of my protein so the top of the protein is pulled so
that the whole protein rotated
Steven Neumann wrote:
On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
Hello Justin,
As you recommended I run longer pulling of my ligand. I pull the
ligand which is on the top of my
Steven Neumann wrote:
On Fri, Feb 17, 2012 at 2:52 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu
As far as i remember for PBC the distance between the reference and the
pulled group are relevant, and not the distance between the reference
group and the virtual spring (place where the pulling potential is zero).
Looking into the code of GROMACS-4.0.7 backs this.
If the distance between the
Dear Gmx Users,
Is it always required to restrained positions of the protein while pulling
your ligand? My system is made of 10 ligands attached to my protein
surface. I am pulling one of them.
I have just seen trajectory of pulling my ligand without restraining
positions of protein and 9
Steven Neumann wrote:
Dear Gmx Users,
Is it always required to restrained positions of the protein while
pulling your ligand? My system is made of 10 ligands attached to my
protein surface. I am pulling one of them.
No, it is not required. I assume you've gotten this idea from my
Steven Neumann wrote:
Thank you Justin. I run my pulling using two force constant for pulling.
K1=100 and K1=200
Please, see attached plots of force vs time. Is there any criteria to
adjust pulling constant? Would you suggest running it for a longer time?
I know of no systematic study for
Thank you Justin!
On Mon, Feb 13, 2012 at 2:44 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Thank you Justin. I run my pulling using two force constant for pulling.
K1=100 and K1=200
Please, see attached plots of force vs time. Is there any criteria to
adjust pulling
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