[gmx-users] trjconv center on protein

[Tsjerk Wassenaar]

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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