>
>
>>
> A pull vector can indeed not be (0, 0, 0) but that's not a pull rate.
The pull vector is exactly as set by you to N N Y, maybe the code
multiplies the vector components by the corresponding pull rates and then
checks the resulting velocity vector, I don't know, but the error is there
On 6/2/17 6:40 PM, Alex wrote:
I find that surprising. Please provide the full, exact error and your
pull settings. All of the geometries should work with zero or non-zero
pull rates. But I admit, it has been many years since I used GROMACS with
the pull code.
Simply take your pull
>
> I find that surprising. Please provide the full, exact error and your
>> pull settings. All of the geometries should work with zero or non-zero
>> pull rates. But I admit, it has been many years since I used GROMACS with
>> the pull code.
>>
>
Simply take your pull code from the tutorial and
On 6/2/17 4:17 PM, Alex wrote:
So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my
I find that surprising. Please provide the full, exact error and your pull
settings. All of the geometries should work
So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my
particular system, the COM position coincides with the center of the single
reactive pore at the geometric center of the membrane. Why even bother with
this
Yes, because if your ion diffuses laterally (or whatever constitutes
your "hole"), then you're not sampling what you think you're
sampling. That's what the cylinder geometry is for. You have a
system capable of significant lateral movement, so if you fail to
apply a bias that acts in
On 6/1/17 6:35 PM, Alex wrote:
You have a membrane with water on either side, yes? That's a layered
system.
But frankly, at this point I don't follow at all what you're trying to do.
-
Let me try from the beginning. :)
A membrane in XY, water on both sides. At the center of the
>
>
>>
> You have a membrane with water on either side, yes? That's a layered
> system.
>
> But frankly, at this point I don't follow at all what you're trying to do.
>
> -
Let me try from the beginning. :)
A membrane in XY, water on both sides. At the center of the membrane, there
is a
On 6/1/17 6:16 PM, Alex wrote:
Your situation is completely different. Look into the cylinder settings
for dealing with a layered system, but I have no experience with them. To
be clear - you always need two groups to define the vector (reaction
coordinate) along which the bias is
>
>
>>
> Your situation is completely different. Look into the cylinder settings
> for dealing with a layered system, but I have no experience with them. To
> be clear - you always need two groups to define the vector (reaction
> coordinate) along which the bias is applied. So you need to
On 6/1/17 4:28 PM, Alex wrote:
Just a few quick questions for Justin.
I am looking at your tutorial, starting here:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
1. In your example, you have two pull groups. My understanding is that both
are pulled
Just a few quick questions for Justin.
I am looking at your tutorial, starting here:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
1. In your example, you have two pull groups. My understanding is that both
are pulled relative to each other. In my case,
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