[gmx-users] gmx wham (again)

[Alex]

... and everything is segfaulting, though worked perfectly fine until the
'cylinder' thing.

On Wed, Apr 18, 2018 at 3:45 PM, Alex <nedomacho at gmail.com> wrote:

> 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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>
>