[gmx-users] gmx wham (again)

[Justin Lemkul]

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 <jalemkul at 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at 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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================