[gmx-users] Restarting problem of tpbconv

[minnale]

Thanks Justin for your prompt reply, now I got the meaning of gen_vel= no. 
Then I tried tpbconv this way still it couldn't work and showed same error mentioned in earlier mail.
tpbconv -f popc.trr -e popc.edr -s popc.tpr -time 6170 (6170 is frame) 
 this 6170 frame number got it from command trjconv -f popc.trr -o popc.xtc
it displays like this
 Will write xtc: Compressed trajectory (portable xdr format)
trn version: GMX_trn_file (single precision)
Reading frame       0 time 1000.000   
Setting output precision to 0.001 (nm)
Reading frame       1 time 1000.200    ->  frame      1 time 1000.200 Reading frame       2 time 1000.400    ->  frame      2 time 1000.400 Reading frame       3 time 1000.600    ->  frame      3 time 1000.600       
    -              -
    -              -  
    -              -
    -              -
Reading frame    2000 time 1400.000    ->  frame   2000 time 1400.000 Reading frame    3000 time 1600.000    ->  frame   3000 time 1600.000 Reading frame    4000 time 1800.000    ->  frame   4000 time 1800.000 Reading frame    5000 time 2000.000    ->  frame   5000 time 2000.000 Reading frame    6000 time 2200.000    ->  frame   6000 time 2200.000  ->  frame   6170 time 2234.000      

gcq#85: "All Beauty Must Die" (Nick Cave)

Any suggestions would be appreciated
Thanks in advance.

On Sat, 27 Sep 2008 Justin A.Lemkul wrote :
>
>
>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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>>
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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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