[gmx-users] there wasn't md_0_1.xtc file

[Justin Lemkul]

On 4/4/15 1:45 PM, marzieh dehghan wrote:
> Hi every body
>
> after creating a covalent bond, I ran output file based on GROMACS tutorial
> (Lysozyme in water) and applied the following command " mdrun -deffnm
> md_0_1". at the end of 1ns, I achieved the following output files:
> md_0_1.cpt
> md_0_1.edr
> md_0_1.gro
> md_0_1.log
> md_0_1.tpr
> md_0_1.trr
> md_0_1_prev.cpt
>
> but unfortunatelly there wasn't md_0_1.xtc file.
>
> please let me know how can I calculate distance, RMSD or RMSF because they
> need to have md_0_1.xtc ?
>

An .xtc is just a trajectory.  So is a .trr.

If you want .xtc, you need to specify so in the .mdp file (nstxout-compressed > 
0 in 5.0 or nstxtcout > 0 in prior versions).

-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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