[gmx-users] gmx wham (again)

[Alex]

In addition, we seem to have a different problem:

-------------------------------------------------------
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
>
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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