[gmx-users] Fwd: Data collection xtc file
alexanderwien2k at gmail.com
Wed Mar 6 12:54:27 CET 2019
Any idea please?
---------- Forwarded message ---------
From: Alex <alexanderwien2k at gmail.com>
Date: Tue, Mar 5, 2019 at 1:10 PM
Subject: Data collection xtc file
To: <gmx-users at gromacs.org>
Here is the data collection part of a simulation's mdp file:
integrator = md
dt = 0.002 ; 2 fs
nsteps = 50000000 ; 100 ns
xtc-precision = 1000
nstlist = 40
;;in .trr file
nstxout = 10000
nstvout = 10000000
nstfout = 0
;;in energy file.log
nstlog = 200
nstcalcenergy = 10
nstenergy = 200
;;in xtc file
nstxout-compressed = 50
The simulation is running and now is in 38753000 step (77506 ns time).
Using the gmx_mpi trjconv I am trying to dump out some frames from the .xtc
file at times t= 71000 ns, t= 75000 ns and t= 76000 ns, however, the
outputs gro files are surprisingly empty. The Precision of out.xtc is 0.001
(nm) and it said that "WARNING no output, last frame read at t=70352.3".
Considering the parameters above I wonder if it is reasonable to have no
stored frame after t=70352.3 to t= 76000 ns?
The Gromacs version is 18.6.
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