[gmx-users] trjconv center on protein

Tomek Wlodarski tomek.wlodarski at gmail.com
Sun May 8 19:30:34 CEST 2011

Dear Tsjerk,

I was afraid that it works like this...
It is possible to "center" the system in a different way? without this
additional component to the water displacement?
What I want is to have protein always in the center of my view
But not by some artificial "centering" inside the box nor changing the
coordination system, just by choosing from pbc those water molecules
which are around protein even though protein is passing through box
edge. So my box would be drifting with protein but coordination system
is fixed somewhere outside the box.
I am not sure if I make it more clear ;)


On Fri, May 6, 2011 at 10:28 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hey :)
> Option -center shifts the system, which will show up as a component in the
> displacement.
> Cheers,
> Tsjerk
> On May 6, 2011 5:39 PM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> Tomek Wlodarski wrote: > > Dear Justin, > > Thanks, sure I will give more
> details. > > This comman...
> Are all the measurements being done in VMD, or are you using g_dist for any
> of these?  If you're using g_dist, then some of the distances may be
> affected by using your old .tpr file, wherein the protein is perhaps not
> centered.
> If all of the measurements are being done in VMD, then I can't comment, but
> perhaps someone else can.  It might be useful to show how you're doing these
> measurements.  If you're not using g_dist, it would be interesting to see
> how the results of g_dist and VMD compare, in order to tease out the source
> of the difference.
> -Justin
>> Best! > > tomek > > On Fri, May 6, 2011 at 1:15 AM, Justin A. Lemkul
>> <jalemkul at vt.edu> wrote: >>...
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