[gmx-users] g_dist error
aiswarya.pawar at gmail.com
Mon Sep 12 13:22:39 CEST 2011
Am using g_dist to find the distance between water and protein. for
that i made a index file such as-
a CA(protein atoms)
a OW(water atoms)
i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35
instead of getting the result for protein-SOL distance . my output
shows SOL-OW distance as seen below-
t: 1 136 SOL 2336 OW 0.772373 (nm)
even after specifying am getting an wrong output.
On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> aiswarya pawar wrote:
>> Hi Users,
>> Am using g_dist to find the distance between water and protein. but my
>> output has the values of SOL-water distance.
>> t: 1 136 SOL 2336 OW 0.772373 (nm)
> This is not a water-water distance, it is the output of the -dist option
> telling you that water molecule 136 has its OW atom at 0.7723273 nm from
> whatever your reference group is.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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