[gmx-users] g_dist error

[aiswarya pawar]

Hi Justin,

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.

Thanks



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
>
> --
> ==============================**==========
>
> Justin A. Lemkul
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> ICTAS Doctoral Scholar
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