minnale wrote:
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
There's no need to use trjconv; check the contents of both the .trr and .edr
file with gmxcheck. It will output which frames are incomplete, so just choose
a frame present in both the .trr and .edr that is complete. Then you can use
tpbconv -time with that timepoint.
-Justin
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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--
========================================
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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