[gmx-users] g_dist

[Justin Lemkul]

On 3/16/15 6:43 AM, RINU KHATTRI wrote:
> hello everyone
>
> I am working on protein complex with popc membrane gromcs version is 4.5.5
> i want to calculate the distance between two residues during the
> simulation (200ns) i have been made the .ndx file of atoms of two
> residues and concatenate .xtc file and final .tpr file
>
> g_dist -f full.xtc -s final.tpr -n atom.ndx -o dist.xvg
>
> Molecule in topology has atom numbers below and above natoms (3893).
> You are probably trying to use a trajectory which does not match the
> first 3893 atoms of the run input file.
> You can make a matching run input file with tpbconv.
>
> the indx file is having the atom no which are present in last.gro file
>
> kindly help

So what does gmxcheck tell you about the contents of the .tpr and the .xtc? 
Likely you have a mismatch in what you saved to the trajectory either in the run 
or when using trjconv at some point.

-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

==================================================