minnale wrote:
Hi all
My system was crashed inbetween simulation, so restarted the run by
using tpbconv command
tpbconv -f popc.trr -e popc.edr -s popc.tpr -o popc_restart -time 2235.2
-until 3000 it showing
Last frame read 6173
WARNING: Incomplete frame: nr 6174 time 2234.600
-------------------------------------------------------
Program tpbconv, VERSION 3.3.1
Source code file: enxio.c, line: 401
Fatal error:
Could not find frame with time 2235.200195 in 'popc.edr'
-------------------------------------------------------
when I view the popc.edr file by using gmxcheck it showing
Opened 3nspop128new.edr as single precision energy file
frame: 500000 (index 0), t: 1000.000
Reading frame 6000 time 2200.000
Last frame read 6173
WARNING: Incomplete frame: nr 6174 time 2234.600
Found 6173 frames with a timestep of 0.2 ps.
its may be due in md.mdp file I am using velocites = no (I am doubting
because read doing restarts webpage and tpbconv -h command I understood
"Note that a frame with coordinates and velocities is needed, which
means that when you never write velocities, you can not use tpbconv and
you have to start the run again from the beginning"
Use tpbconv -time and specify a frame that actually exists.
Note that gen_vel = no is completely separate from nstvout = 0. If you use
gen_vel = no, it implies that the simulation is continuing from a previous run.
If you use nstvout = 0, you are never saving velocities, and thus tpbconv will
not work.
-Justin
Could give me some suggestion how can I restart the crashed simulation?
Thanks alot for any suggestion.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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