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

Yun Shi yunshi09 at gmail.com
Wed Feb 20 17:01:58 CET 2013

Hi Justin,

I was not able  to find relevant posts in the archive. Any special
keyword for searching?

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?


On Wed, Feb 20, 2013 at 5:16 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 2/20/13 1:14 AM, Yun Shi wrote:
>> Hi all,
>> For the purpose of calculating deltaG from umbrella sampling, I have
>> first pulled my ligand away from the enzyme active site along an
>> arbitrary direction (say x axis), setting the enzyme as pull_group0.
>> But I found the ligand was moving in the yz plane while pulling along
>> x, which I guess is not uncommon. Then I wonder which distance to use
>> a reference for the definition of umbrella sampling windows. Would
>> that be better to stick to the x component of protein-ligand distance,
>> which I can easily read from pullx.xvg file while ignoring the y and z
>> components? Or is it still better to use g_dist to calculate the
>> absolute protein-ligand COM distance and use it for spacing reference?
> If you have motion in all three spatial dimensions, I would think that
> ignoring deviations in any of them is inappropriate.  Single-dimension
> reaction coordinates only make sense if the desired path is linear along one
> axis.  If you're pulling something out of a binding cavity or channel that
> is not exactly linear, that complicates matters.  There were some nice
> explanations of practical considerations for such simulations a few months
> ago, so do check the archive.
> -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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