[gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 4:39 PM, chinnu657 wrote:
> I'm basically trying to see how the distance between the ligand and protein
> changes with time using their centres of mass and the only way I've come
> across is by using g_dist.
>
> I'm pasting the contents from the terminal after the doing a gmxcheck on the
> md_0_1.xtc file which is my .xtc file from the production simulation.
>
> Checking file md_0_1.xtc
> Reading frame       0 time    0.000
> # Atoms  33037
> Precision 0.001 (nm)
> Last frame       1000 time 2000.000
>
>
> Item        #frames Timestep (ps)
> Step          1001    2
> Time          1001    2
> Lambda           0
> Coords        1001    2
> Velocities       0
> Forces           0
> Box           1001    2
>
> can I attach the index.ndx file again? Was this what you were looking for?
> index.ndx <http://gromacs.5086.x6.nabble.com/file/n5010738/index.ndx>
>

Better would be for you to actually tell us what groups you chose (actual screen 
output from the selection would be best), rather than leave us to scroll through 
and guess.  If md_0_1.xtc has the whole system (33037 atoms), in principle that 
error should not have occurred.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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