[gmx-users] Distance for window spacing in US?

[Yun Shi]

So in umbrella sampling, does it really matter if the vector
connecting the COMs of protein and ligand is NOT parallel with the
vector of the pulling force (although the pull rate is 0)?

I guess as long as the force in each sampling window is along the same
direction, we can in theory get potential of mean force along any
direction.

Thanks,
Yun

On Wed, Feb 20, 2013 at 1:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/20/13 11:01 AM, Yun Shi wrote:
>>
>> Hi Justin,
>>
>> I was not able  to find relevant posts in the archive. Any special
>> keyword for searching?
>>
>
> I'm afraid I can't think of anything magical off the top of my head, no.
>
>
>> But I wonder if it would introduce any additional error to deltaG
>> calculations if I restrain the dissociation pathway to x axis, using
>> pull_vecl = 1 0 0. Would the program then forcing the velocities along
>> y and z axes to be zero?
>>
>
> No.  If you choose the restraint direction to only coincide with x, then
> restraint forces are only applied along x.  That does not mean there can be
> no motion along y and z.  You have to decide on a suitable dimension or set
> of dimensions based on the geometry of your system.
>
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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