Re: [gmx-users] g_dist output error

[aiswarya pawar]

hi Justin,

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.

Thanks

On Mon, Sep 12, 2011 at 4:53 PM, Justin A. Lemkul  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
>> 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)
>>  can anyone tell me whats wrong with this.
>>
>
> Please see my previous message.  This is not a "SOL-water" distance.
>
> -Justin
>
> --
> ==**==
>
> 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
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] g_dist output error

[Justin A. Lemkul]

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 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)
 can anyone tell me whats wrong with this.


Please see my previous message.  This is not a "SOL-water" distance.

-Justin

--


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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_dist output error

[aiswarya pawar]

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 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)
 can anyone tell me whats wrong with this.
Thanks
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