[gmx-users] Restarting problem of tpbconv

[Justin A. Lemkul]

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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