[gmx-users] Problem with gmx-distance

[Justin Lemkul]

On 9/16/15 9:06 AM, Timofey Tyugashev wrote:
> I want to get the distance between atoms 3770 and 5182 in my trajectory
> After consulting with the Manual I write command:
> gmx distance -n ind2.ndx -f trj1_WT_md_40.xtc -s wt_md.gro -oav distav.xvg -oall
> dist.xvg
> and index file ind2.ndx:
> [ LYS_241_ODG_C1' ]
> 3770 5182
>
> The program responds like this:
>
> Available static index groups:
>   Group  0 "LYS_241_ODG_C1'" (2 atoms)
> Specify any number of selections for option 'select'
> (Position pairs to calculate distances for):
>
> If I pick 0, it responds 'Selection '0' parsed' and then nothing happens.
> What to do next? The manual is incredibly murky and there are no examples in the
> net.

Your atoms can't be in the same group.  That was the same as with g_dist.

[ atom1 ]
3770
[ atom2 ]
5182

gmx distance -n -f -s -oav -oall -select 'com of group "atom1" plus com of group 
"atom2"'

See "gmx help selections" and specifically "gmx help selections examples" for 
syntax of selections and a few simple examples.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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