[gmx-users] g_dist output error
aiswarya.pawar at gmail.com
Mon Sep 12 13:47:51 CEST 2011
As far i referred the OW,HW1 etc are water atoms so how can it be distance
between the SOL protein atoms, instead it is SOL water atoms.
On Mon, Sep 12, 2011 at 4:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> aiswarya pawar wrote:
>> Hi gromacs Users,
>> 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
>> 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)
>> can anyone tell me whats wrong with this.
> Please see my previous message. This is not a "SOL-water" distance.
> 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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