On 4/18/18 4:08 PM, Alex wrote:
In addition, we seem to have a different problem:
Cylinder geometry requires the use of pull-coord1-vec, not pull-coord1-dim.
-Justin
-------------------------------------------------------
Program: gmx grompp, version 2018
Source file: src/gromacs/gmxpreprocess/readpull.cpp (line 234)
Fatal error:
With pull geometry cylinder the pull vector can not be 0,0,0
On Wed, Apr 18, 2018 at 6:34 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 4/18/18 3:17 AM, Alex wrote:
I suppose this question is mostly for Justin...
Let me remind what I am dealing with and ask if my idea is correct.
I have a rectangular membrane in XY with a pore at (X/2, Y/2) in water
and want to get the Gibbs free energy curve for an ion. For this, I have a
bunch of starting configurations at (X/2, Y/2) and Z varying between some
-z0 and z0. The bias in the "fake" pull mdp is applied as N N Y. Near the
membrane, this means the entire plane is sampled, which adds contributions
I am not interested in. I want the pore and a small region of the membrane
around it, not the membrane, given its properties.
So, I applied weak (k=50) in-plane restraint to the ion for each of the
sampled configurations -- to keep the sampling region a bit closer to the
pore. The results look completely different, but they finally make very
good qualitative sense. The ion still walks around within a small disk, but
not much -- this tentatively makes me happy.
Would you believe the results obtained this way, assuming otherwise
proper setup?
This is the exact situation that the "cylinder" pull geometry is designed
to model. I suggest going that route rather than ad hoc restraints, which
will influence the PMF and should be otherwise accounted for.
-Justin
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
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jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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