On 10/9/12 9:45 AM, Ali Alizadeh wrote:
Dear All users
I ran energy minimization and mdrun for my system with
EM was a good run :
Run parameters
integrator = steep
dt = 0.002
nsteps = 50000
emtol =100
MD was not a good run :
integrator = steep
This is not MD, you're running energy minimization again.
dt = 0.002
nsteps = 50000
emtol =100
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
nstxtcout = 100
xtc_precision = 100
This was not converged! then increase emtol to 3000
Terminally it was converged for my mdrun,
But All of the my output files, for example hnum.xvg(g_hnum), are empty. Why?
No clue. You haven't shown us your commands or proved that there's anything
useful in your trajectory files (e.g. from gmxcheck) that you're analyzing.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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