[gmx-users] Restarting problem of tpbconv

[Justin A. Lemkul]

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

========================================