# [gmx-users] gmx wham (again)

Alex nedomacho at gmail.com
Wed Apr 18 23:45:14 CEST 2018

```Which then would be = 0 0 1, correct? This though will have to coexist with
pull_coord1_rate        = 0.0

Is that reasonable?

Thanks,

Alex

On Wed, Apr 18, 2018 at 2:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
>
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> Gromacs Users mailing list
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```