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.
>>
>>
>>
>>Rediff Shopping
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>>
>>
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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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