[gmx-users] Problem with gmx-distance
jalemkul at vt.edu
Wed Sep 16 16:00:48 CEST 2015
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
> 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
Your atoms can't be in the same group. That was the same as with g_dist.
[ atom1 ]
[ atom2 ]
gmx distance -n -f -s -oav -oall -select 'com of group "atom1" plus com of group
See "gmx help selections" and specifically "gmx help selections examples" for
syntax of selections and a few simple examples.
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
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